Whats worse ? the destruction caused by religion? or the destruction caused by atheism..?

I know of no destruction that was caused by atheism. Your suggestion that some people in history (not all of whom were atheists) caused destruction because of atheism is akin to saying they were destructive because they all have Y chromosomes. None of them acted in the name of atheism. And as you point out, religion clearly doesn't stop people from being destructive, but it does often give them cause to be.