One of the lamest arguments (actually a fallacy) of religious apologists when confronted with atrocities done in the name of religion is to throw back the accusation at the opponent. It usually takes the form of bringing up supposedly atheistic regimes such as Stalin's Soviet Union or Nazi Germany (ignoring for the moment that the Nazi State wasn't "atheist"). The problem is, even if atheism is the cause of atrocities or worse atrocities, this doesn't address the point in the slightest.
The point being, of course, that religion has seemingly motivated violence, persecutions and killing (even though we are repeatedly informed by theologians and other religious apologists that religion is a necessary source of morality and that the god/gods of these religions is "good"). There is nothing in this particular charge against religion that says it is the sole cause of violence or persecution, but simply that it is a cause of such things, and that therefore it may be that its elimination would be all to the good. That is what the believer must address.
As to atheism, it is not in any way a worldview in and of itself, but just lack of belief in something (gods). Atheists as a group don't generally agree on much outside of that lack of belief, not even on the subject of materialism, which many wrongly assume is part of atheism. An officially atheist government, like the totalitarian Stalin regime, must therefore have something else behind its motivation to cruel actions than simple non-belief in a god (I know some will say that's all you need, following Dostoevsky, but the opposite is actually the case, i.e., if God exists and you are His follower, anything is permitted, including burning heretics at the stake or flying planes into the skyscrapers of the infidels).
No, what you need is a collectivist faith, such as Marxism-Leninism (which even has its own holy scriptures) to commit such horrendous acts.