Historically there's been more bloodshed from in-fighting among sects within a single religion or Emperors and Pharaohs showing favour to their own gods to consolidate their power.
The idea of people in the same religion fighting on one side against another is very Euro-centric and is maybe only true during the crusades , through to the conquest of Byzantium by the Ottomans, even then, Western Europe didn't care all too much, as the Eastern church wasn't with them and even the Medici's failed to unite the two churches. The sacking of Byzantium by the crusades on the urging of Venician interests is probably an interesting chapter of christemdom that's not often discussed. But it was responsible, quite literally, for fuelling the nascent renaissance in Europe at the time as the wealth of the east poured into the medieval west.
I'm not opposed to religion, but most serious analysis of the feature as applied in Civ4 point to it being fairly modest and interachangeable and heavily human centric in its implementation. (ie: The AI can never switch to any safe religion because human players won't care what religion the AI is on; It's only AI players who places undue weight on the human player having the same religion as they do, which is why it is a 'crutch' mechanic to smooth overly diplomacy.
I actually beta'd early builds of Civ4, before this crutch was put in and before vassal states, the dev team wanted to create a 'bloc' system where half the world is constantly at war with each other, either cold or hot, and they wanted to way for alliances for form so the original design was to seed AI's in such a way that half the world would just not like you, or trade with the player, while the other half did like you or rather, disliked you less. This way players would naturally steer towards civs that liked them, and hate civs that did not. But the problem of course is if you drew those half of civs who hated you as your neighbours, it crippled your early game. This system actually was released in vanilla, which made early diplo wins nigh impossible without warfare and what came to be known as domination-lite. Vassals was therefore brought in to address it, though I wasn't involved with warlords testing, I can only assume on that point.
But essentially, the Civ4 team never solved the core diplomacy challenge they wanted to give the players. Through many patches, the bloc system was toned down into a more malleable generic system where mercenary Civs were willing to war and peace based on set and easy to meet conditions. The Civs absolutely also lacked flavour. They were all very genreric and generically referred to as 'AI civ neighbour' it didn't matter which, they all behaved the same diplomatically.
Lastly, I don't even have an idea of where Civ5 might end up. There's a religion value for AI civs in the xml. It's likely a leftover from the Civ4 core that the Civ5 team built the xml on, but it may come back.
