This is troubling to many atheists I have known. They believe that theists tend to favor "Kill them all. God will know his own."
Of course, when two or more groups with differing ideas decide to kill thim all, it gets downright historical.
It is telling that an atheist would even bother to seek a justification or excuse for his own disbelief.
My Spiritual discernment on such conduct is that they are more likely spiritually rebellious or doubtful than actually disbelieving. A "true" atheist, IMHO, is a metaphysical naturalist who doesn't believe but doesn't mind if you do - he seeks no justification and makes no excuses.