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I agree with you that it isn't God that is the problem - God is just an argument over whether something exists or doesn't, it is like saying that a belief in unicorns kills people.
The main problem is faith. People so sure they are right, they will do anything to make sure that they win. That is why religion is often such a strong feature in the worst excesses of humanity, it is not the religion itself, it is the faith.
I mean, take Stalin, he went through the seminary and ended up an atheist, and ended up being pretty much the same kind of person as Hitler, who proclaimed himself a Christian and used religion pretty extensively to whip up his supporters. Both had absolute faith that they were right, both were willing to use any means of propaganda to do it, and both ended up killing a lot of people.
Faith is not always religious, it is simply that state of mind that goes "Damn the evidence" and proclaims itself right. It is encouraged in religion, because religion frequently rests on belief without evidence, but it isn't the only place where it is found or encouraged.
Doubt is far more valuable than faith.