I don't like the "active gods" approach to fantastic religions that is characteristic of the Forgotten Realms and Greyhawk settings. In fact, I loathe everything about it. The Eberron campaign setting was a major wake-up call for me because it was the first time I was exposed to a D&D setting that handled religion in a way that I recognized as having some recognizable relationship to what I observe in the real world. Eberron uses a "distant gods" approach, where people don't remember the afterlife, and they don't get to sit down and have a beer with Jesus. Instead, they believe various things about what happens to us after they die, and argue about it.
This is basically consistent with how people act in the real world. I'm not particularly religious, but my lack of personal spirituality does not prevent me from recognizing that religious faith is an important motivator for many people all over the world. Many people believe in a god or gods. Many individuals who don't believe pretend to believe in order to make people of faith like them, or to avoid persecution. It's frankly unlikely that anyone could currently be elected president of the United States if he or she were openly atheist. I'm not convinced that a Jewish, Hindu, or Muslim president is electable in the USA, even. Despite laws to the effect that religious creed should never be part of the prerequisites for elective office in the US, the highest echelons in American politics are pretty nearly reserved for people who purport to be some kind of Christian. Faith genuinely matters to a lot of people. It informs all sorts of major decisions.
The prevailing approach to religion in fantasy gaming appears to be about as far from the real world as it's possible to get. If you're playing in the Forgotten Realms, your character can obtain access to magic that allows him to travel to whatever part of the afterlife pertains to his patron deity, see what happens to the souls of the faithful, and even consult his god on matters of significance. There is no actual place for faith in this scheme. If you claim to have met a god, you may be accused of being a bullshitter, but people aren't going to think you're a madman. You also aren't going to have a Protestant Reformation. Or a new religion. Or a schism in an existing one.
Things get even weirder and less tenable once you start assigning power levels to your various gods, often based on the number of people who worship them. This makes the deity dependent on the worshiper, rather than the worshiper dependent upon the deity. It pretty much turns the world upside down, in terms of how religious sentiment can be expected to operate.
All this said, if you use a distant gods approach in a D&D setting, it still presents a few issues. For one, your religions now have to have doctrines. They have to have articles of faith. They have to have, in short, actual stuff the faithful believe. It's no longer sufficient for a religion to consist of doing whatever it is that your deity told the high priest is in order during their weekly tea, biscuits, and game of cribbage.
For another, you have to have some idea of what will happen when believers in the same religion have some kind of major disagreement about matters of faith. Is that a heresy? A schism that results in two different branches of the religion that are hostile to one another? Realistically, the difference is usually that it's a heresy if you're part of a minority that is small enough for the "orthodox" part of your church to kill you for believing the wrong thing, and it's a schism if you belong to a group that is big enough or powerful enough (or protected by someone who is powerful enough) to make it a problem to kill you for believing the wrong thing.
And for a last, you have to figure out to what degree all of this is going to have an impact on the mechanics of your game. The idea that it will impact your game is pretty solid though. There's a section at the very end of the cleric class material that reads as follows:
A cleric who grossly violates the code of conduct required by his god loses all spells and class features, except for armor and shield proficiencies and proficiency with simple weapons. He cannot thereafter gain levels as a cleric of that god until he atones (see the atonement spell description).
Based on the quoted material, I think it's clear that clerics are supposed to lose their powers if they are not basically obedient to whatever their gods require of them. That's really straightforward if you can go to Heaven, talk to God, and come home to put into practice whatever advice you glean during the visit. It's much less straightforward when you can't have that sort of Q&A session.
One approach you can take with this is, I guess, that the code of conduct for clerics of a particular religion is derived from whatever is the mainstream doctrine of that religion. So (for example) bearing false witness is probably against the code of conduct for a priest of a goddess of law. That's probably not a controversial idea; there are clear, practical reasons why you don't like falsehoods if you're concerned with anything to do with the administration of a legal code. But more controversial might be the stance of a religion, devoted to a goddess of fertility, toward homosexuality—or contraception. I think that there are grounds for dispute as to how such a deity ought to feel about sexual activity that cannot be expected to produce new life. So the two sides of that dispute would, we can suppose, argue about it, maybe even coming to blows, until one side wins or it becomes clear that neither side is going to, and the church splits.
That's all fine from a roleplay and world building point of view. In fact, it's great! Now we have an example of an in-game religion that actually behaves somewhat like a real one. But there's another question, which is whether or not the clergy of this religion would have differing powers as a result of their stance on this dispute. That is, if a cleric of the fertility goddess thinks it's okay to be homosexual, then would this person get access to a different set of cleric domains than would be the case for someone who sides with the branch of the church that doesn't think it's okay?
The answer may not be a resounding yes or no. I think that there's room for it to be the case that these clerics' theological differences won't have mechanical consequences. But let's consider, at least for a moment, the possibility that the deity we're talking about is an "earth goddess" with a concern for fertility. She's basically an agricultural deity, in this case, but people also consult her priesthood around issues related to family planning and procreation. We'll say that she's a figure kind of like Merthia from the Tolrea setting, except we'll skip the Good domain and give her the Water domain instead, and make her alignment TN. So clerics of any alignment can serve her without violating the "one step" alignment rule for clerics in the Core rules, and she grants access to the Animal, Earth, Plant, and Water domains. We'll also say that without exception, clerics of this fertility goddess turn/destroy undead and spontaneously cast cure spells, regardless of their alignment, because it seems a little odd that any cleric of a deity so concerned with fertility and life would consider the undead anything other than abominations to be destroyed.
Let's recall that by convention, D&D settings do not rely on science the way we understand it. So people aren't necessarily going to know that plant life has a sexual component to its reproductive cycle. It may be that the substance of this fictitious schism might be that the homosexuality-negative branch of the church pointed to animal life specifically as evidence that the goddess favors male/female pairings, because those are what lead to procreation, and the homosexuality-positive branch of the church countered by saying that this is baloney, because look! Plants are fertile without having sex at all!
In any event, we end up with a scenario where both groups of clerics worship the same goddess, and they even still have a lot of doctrine in common. They are recognizably members of the same religion, but now there are two denominations in the religion instead of just one. In such a case, might not the homosexuality-negative adherents of this fertility goddess begin to express different powers? Perhaps they retain access to Animal, Earth, and Water, but lose Plant. Since they are good at dealing with animals, we'll call them Husbandmen. And perhaps the homosexuality-positive branch of the church loses Animal and retains Earth, Plant, and Water. We'll call them Farmers. It's a plausible scenario, at least. We could even go so far as to grant a new domain to one or both of these new denominations. Maybe the Farmers get access to the Sun domain, reflecting their concern with plants and crops. I don't know what the Husbandmen would receive, or even if there is any addition that makes sense for them. It's not really important, at least for the sake of this discussion. I guess I also should point out that we don't have any reason to think that the Farmers are all gays or lesbians. They just don't think homosexuality is a sin in the eyes of their goddess.
But we're more interested in exploring the idea that these people are still members of the same religion. If that's the case, then what does the code of conduct for these clerics look like? Since we've established that their goddess is a fertility deity, there's potentially some ground for us to say that regardless of whether they are Husbandmen or Farmers, homosexual or straight, they're not going to be fans of contraception. It may be that Farmers are very concerned that if you do engaged in homosexual behavior, you're specifically not doing it to avoid having children. So if a cleric of this faith employs contraception, maybe that's a "gross violation" of the code of conduct that would actually cause him to lose his powers until he receives an atonement spell. Or maybe the line is drawn further out, and it's a problem to administer contraception to other people. Maybe Husbandmen and Farmers also agree that abortions are wicked. Of course this is just an example, but it's at least an example that's pretty easy to reason through.
Another thing to consider, I guess, is how all of this stuff might play with laypeople in the same religion, as well as with outsiders to the faith. If we assume that this religion's clergy are involved in outreach to the community, it could be the case that the Farmers might get quite a little political and economic boost once they're the go-to faction if you want help getting your crops to produce well. The Husbandmen and their Animal domain power are fairly useful (they can talk to animals for a few minutes every day), but that's not really going to feed and clothe a bunch of people—they aren't going to make your herds multiply faster or anything like that. But being able to cast plant growth, even from a scroll or wand, turns the clergy of the Farmer denomination into an economic powerhouse.
And what happens if all of this religious turmoil is set against the backdrop of a kingdom ruled by someone who has a same-sex lover? If the Husbandmen denomination concludes that homosexual behavior is a sin, they're going to be treading on very thin ice with such a monarch. Or on the other hand, what if they're active in a warlike kingdom that is neighbor to such a place . . . maybe they've just handed that ruler a divine excuse for a war of conquest against the Pervert Queen of Elbonia!
There's also the matter of heretics. This would be a case where a small number of adherents to a faith believe something that goes against the doctrine of the mainstream faith. Let's take the hypothetical that our original TN fertility goddess, granting access to Animal, Earth, Plant and Water, is also venerated by a heretic who sees her concern with fertility in terms of a cycle of life and death. If you want fruitful herds and plentiful crops . . . you sacrifice to her. Maybe he secretly begins to promulgate this mystery to a few carefully chosen disciples, and forms a cult-like secret society that loses access to Earth in favor of the Death domain. Maybe some of them, if they're evil or neutral aligned, can opt to rebuke/command undead and spontaneously cast inflict spells. We end up with something very similar to one of those mystery cults to Cybele or Diana in the real-life Near East, in this case. And because these heretical priests are able to select either Animal or Plant, they could go undetected for a long time within either the Husbandmen or the Farmers.
I kind of needed to think through this because someone asked me to clarify some things about what his character did and didn't know in the Tolrea setting, and I realized that it was going to be a complicated discussion.