I would tend to ask "How many of these wars and atrocities were actually less about theological disagreements and more about secular power and economic advantage, with religion being a rationalization to cover the real goals?"

All of 'em, Don, every single one. I'm a rabid atheist (according to some), but I know that arguments that claim that things "are done in the name of religion" (or atheism, come to think of it) are generally eyewash. There are plenty of arguments against religion already that don't require bringing in holy wars and the rest.