Well first off the Colonization of Africa most certainly had religious under tones to it. Secondly I will give in to the fact that not every war had religious causes or used religion in the justification of war. However with that said, if you are hard pressed to find a war that didn't have a religious cause or justification through religious means, then are you not proving my point that religion truthfully is a cause or reason for war. Whether or not this is morally right or wrong is not my argument, my simple argument is that leaving the war part of religion out of a game that emulates history is simply a lie. Pretending that religion had no military actions carried out in its name is simply pointless and moronic. Religion throughout its history is the history of war for most purposes, so why not emulate that in the game. Yes as I said give some sort of bonus for being peaceful but also give military bonus for being war-like.
Also I am not even saying war is half the object of religion, I am just trying to suggest a way to emulate reality, if that means exaggerating slightly then so be it, if it not only enhances game play but also brings us closer to realism then what is the problem. Also if you want to emulate reality even better just lower the chance of the AI from choosing that side of the religion, that way only a few civs would have been war-like.