I tend to agree.
It seems people seem to commit atrocities out of passionate attachment for something be it a deity or a nation state. I don't think it would be too much of a stretch to consider atrocities either on a small scale or a large scale crimes of passion. Since religion is a function of emotional expression it's not too difficult for unscrupulous individuals to push people to commit atrocities in the name of religion.
And indeed, since atheism is, by definition, a lack of belief in a deity it follows that there is no emotional attachment to inflame that which might result in such crimes. And yet, every atheist I have ever met or heard about, including myself, is human. And humans have emotions. I find it difficult to believe that atheists are so perfectly rational and atheism such a panacea for the extremes of human nature that it would be impossible for an atheist to engage in an atrocity in the name of atheism. Theoretically, if enough atheists cared enough about atheism they might be driven to do some pretty horrible things in the name of that ideology.
Of course after the fight starts it doesn't matter who's right, only who's left. So if atheists respond in kind to the assaults of those whose ideologies differ from their own, I don't really consider that so much a defense of atheism but simply defense. Any atrocities committed for any reason are wrong, no matter the ideology in question. A more interesting paradox is the possibility of a group of atheists initiating violence in the name of atheism.
It is possible to have a religion without a deity. As long as a group feels the same way about something and possibly conducts some sort of organized ritual to share that feeling, you've got yourself a religion. Such activities could include anything from a Pentecostal revival to a baseball game. In fact, the greatest threat to religion today isn't atheism, but professional sports.
So the question might be how do we take the emotional involvement of atheists and direct it in some other way than toward something they do not believe in? Well, most of the time your average atheist values reason and science. This might be a popular response to the common disregard of of same by most religious institutions throughout history who had a tendency to barbecue people who disagreed with them on rational grounds. Be that as it may, it might be a good place to start to look for such an impetus.
There has been an ongoing controversy regarding whether Communism was atheistic or religious. I consider it a religion built on a cult of personality. But Communism purported itself to be scientific and rational in nature, based on the inevitability of historical materialism. If any religion could be grounded in the stuff of reality, communism was the largest scale attempt to do so. It seems to me that if one wanted atheists to commit atrocities one would have to channel their emotional attachment to rationality and empirical evidence to give them something to fight for. But that's the catch - communism wasn't just a religion devoted to rationality, but a cult of personality centered around Marx and Lenin and whoever else would do at the time. It seems that, in a way, it might start out as atheism but become something else before the fighting started. Of course there is nothing to keep atheists from committing atrocities in the name of nationalism. Who knows how many atheists participated in the My Lai massacre for instance.
It seems to me that when it comes to matters of faith atheists are cultural anarchists. They seem to be against everything everybody else seems to be for. While there seems to have always been some sort of religion, there have always been a few atheists causing existential problems, and usually getting burned alive for their trouble. Given the trajectory of human cultural development, not believing means not cooperating. And cooperation is essential for the creation of a numerically significant group of people to perpetrate an atrocity of any consequence. So while it is theoretically possible that atheists, being human, are capable of committing atrocities, atheism by its very nature does not lend itself to the kind of cohesion required to generate sufficient focused passion for the ideology to commit such offenses. But that could change.
Religion, as we currently understand it, is on the wane. As societies become more advanced, religion seems to become redundant. But the human tendency toward emotional attachment shows no sign of waning any time soon. In fact, we produce so many sources for emotional attachment now that one of the greatest problems of our modern culture is not a lack of faith, but anomie from an excessive dispersion of faith. Our technological culture can produce and put into motion systems of thought and action just like any other widget. Such man made systems could possibly be ripe ground for the flowering of a sort of atheism not unlike the explosion of transcendence in the axial age two thousand years ago. Maybe. If that's the case, those who believe in the guy with the white beard in the sky may have good reason to cuss us for the next few thousand years.