That's an interesting question, and one which I'd like to take seriously.
Correct me all along here if I'm wrong, because I'm struggling even to get the conceptual framework in place here:
Before Voltaire and his crew the late 18th century, I don't think there were people in Europe or America who would have called themselves "atheists," a term which would have been used only as a denunciatory label applied to an opponent, meaning either "morally bad" or "heretical." And I don't think there was anything like open, organized atheism until the French Revolution.
So you're dealing with a phenomenon which has only been a force in history for less than 250 years; unlike, say, the Judeo-Christian movement which has 2500+ years' worth of history to poke around in looking for vice and virtue.
OK, so looking at the movements or parties which represented atheists' ideals and aspirations since they got out of the salons and into the historic cavalcade, you've got:
It looks like --- other than Nietzsche and Ayn Rand --- a pretty Left-wing line-up.
Now, I don't want to blame atheists unfairly for everything from the Reign of Terror to the British CND, but those are the only organized movements of atheists I see on the world stage.
In all sincerity, I ask: if we are not to judge atheism by its organized historic manifestations, how are we to judge it?
Admittedly, atheism is much more often associated with the left. Conservative people tend to have organized religion as part of the framework of their conservatism.
You have an interesting list there, but besides the Marxists/Communists, the only one I really associate with mass violence is the French Revolution. I thought most Americans regarded that as a "good thing", overthrowing monarchy in favor of republican forms of government has been very messy, but it has been part of the path of progress.
The other things you mention seem to be in the tradition of Europeans always wishing to fight each other over something, whether it be different flavors of Christianity, or Christians versus those who would throw off Christianity. If you want to judge atheists by the worst among us, then allow us to judge Christianity by its most infamous practitioners as well. Or, we could just both admit that social change in bygone years was accompanied by far more violence than Western civilization will tolerate today.
Also, if you are trying to compare the negative impact of Christians to those of atheists—which I believe is an exercise in futility, but nevertheless—you also have to consider the respective population sizes and advances in technology and statecraft that have allowed repressive regimes to be far more viciously effective in the past 100 years than in the 1,900 years of Christian history before that.
If the medieval despots had wiped out tens of millions of their subjects, there would not have been anyone left in the country to rule over!