Sometimes that happens. That's a particular problem with some applications of religion, or anything adopting some religious like elements (stalin's soviet union, north korea etc.).
I believe if you took 50 secular societies and 50 moderately religious societies, you'd have less suffering and less conflict in the secular states, to an extent. Quite often then, such violence uses religion as a means, there would be plenty of other reasons to engage in wars and repression without religion. Even if the leaders of the violence genuinely believe their religious justification, that doesn't mean that other events of similar scale wouldn't have occured. There's also the issue of countries that substitute the state for religion (Though you could argue that the state is the religion), and that can be even more deadly.
Basically, I think religions true role in conflicts is overstated. Religion in society is so pervasive that practically any ill can be blamed on it. I think if we were somehow able to completely rid the world of religion, you'd be suprised how many conflicts still arise for completely secular reasons. They may be different conflicts, but conflicts nonetheless.