Here's the key point, I think: There's nothing in the argument against the existence of a god that justifies that type of behavior. There's nothing that the Red Shirts could point to in evolution, or in physics, or in the logic and reasoning used by atheists to make their case, to say "Hey, this principle tells me it's morally OK to commit this terrible act."

Though if your point is simply that there are bad militant atheists, your point is well taken.