Its pretty difficult to justify murder with a negative position on a claim. That just doesn't make any sense. An atheist can subscribe to many types of philosophy whether its communism, secular humanism, nihilism etc. Many of them you can justify atrocities with, but that justification doesn't in and of it self come from atheism, because a negative position on a claim by another person doesn't easily translate into any justification for anything, because it only deals with one thing, which is the rejection of the claim by theists.
What you should look at is the actual philosophies that said atheists posited and critique them vigorously because any philosophical or theological framework that allows for unjustified and unreasonable use of force, should be rightly derided by everyone.
