I wonder about that. Frankly, once the issue of "My god is the true god" is gone, what reason would most churches in the forgotten realms have to fight?
Is there going to be more than a philosophical discussion about whether or not Chauntea is greater than... is Lathander the God of the Sun? Or the church of Tymora (luck) getting into a fight with the Church of Waukeen (trade and economics)?
Sure, Bane and Cyric and the other evil deities (that frankly should be much less powerful than their good counterparts since so many fewer people would choose to worship them) are going to be causing a lot of conflict, but that is less religion causing conflict than "The being we worship wants to rule the world and we will kill people until that happens" there is no grey, like with the religious wars we had in this world, one side is clearly evil and is recognized as evil by an objective cosmic array.
So, the few churches actively seeking death cause problems, but the majority should get along, at that point we end up moving far closer into politics causing the majority of problems rather than the churches, because church politics and jockeying for power is less about getting worshipers and proving the power of your deity than it is honoring your deity by claiming more stuff in their name.
I guess what I'm talking around is church causing conflicts because of church politics is not what I would consider a religious conflict, a religious conflict is more when the idealogies clash, and that is far less common in the realms once you move beyond the evil gods.... who really could be better served by being something other than gods generally.
Well, I think that the followers of the evil gods would be enough, but there are some schisms within some of the churches as well, such as Oghma. I get what you're saying though.
To me, though things like the Crusades were "religious" wars, or at least that's the reasoning used behind them at the time. So the wars started by the Zhentarim, at least in the 1350's with Fzoul and the church of Bane would be what I would consider a religious war. The same applies to the wars in Mulhurand, Unther and Chessenta, although they are transplanted from another world with Egyptian and other gods (not a Greenwood element). The part that I liked about that implementation was the God Kings called the prime plane native.
As far as the power of the evil gods (or the gods in general) - the idea of the god's power being tied to their faithful started with 2e. The thing is, the way religion is described, the people acknowledge the gods more than actively worship them. Yes, there will be prayers, potentially sacrifices, and celebrations for the gods to some degree or another. So sailors pay homage to Umberlee before setting sail to appease her and hope for a storm-free journey. That sort of thing. So does that count as worshipers? How much do they have to acknowledge them? Is evil stronger than good in general? Is a blood sacrifice more potent? Perhaps the devotion of the faithful is measured, and the followers of the evil gods are more fanatical? There are a lot of possibilities.
Despite 2e setting it up so the power of faith is important to the gods, I don't concern myself with the gods themselves in my campaign. I'm not really concerned whether Bane is a greater god or a lesser god. Nor do I see any in-world difference between the cleric of a demigod and a greater god. My focus is on the churches and the people themselves. What impact they have in the campaign.
One of those factors is that there are always those that want to believe in something. And even if they are a smallish part of the population, they are still susceptible to somebody with great charisma, and a cause. And a religious cause, at least in my mind, will generally pull in more fanatics than a political one. Regardless of whether it's actually a religious conflict, or driven by a despot who is using faith and religion to further his own goals isn't really the issue. Because if the rank and file, the followers, believe it to be a religious war, then it effectively is.
It's absolutely true that the churches of Bane, Cyric, Bhaal, and Malar are going be behind much of the conflicts. In my own campaign, the church of Bane, some Red Wizards of Thay (for whom Bane is the state religion), and a powerful new Zhentarim leader are all working together. Only the church of Bane is really doing so for Bane, and all three of them are plotting, scheming, and moving against each other. But those alliances, however fragile, are causing an awful lot of strife in a particular area of my Realms right now.