While the headline bullet points I can go along with (except #1, nothing is done "in the name of atheism". Thats just retarded. Stalin and Mao didn't do what they did because they were atheist, they did it because they were assholes.)
Counter Point:
He is arguing that you CAN do terrible things in the name of either one, which is pretty much undeniable. Reread what he says there:
"All I need from you is agreement that it's entirely possible for either an atheist or theist world to devolve into a screaming murder festival. The religious leader sends his people into battle because he thinks God commanded it, the Stalins and Maos of the world do the same because they see their people as nothing more than meaty fuel to be ground up to feed the machinery of The State. In both cases, the people are equally dead. "
His fault here isn't logical, it's that he didn't directly realate it to the opening point, which makes it seem illogical. We all know you can do terrible things in the name of either one, fuck, you can do terrible things in the name of anything.
Looking for examples from history off the top of my head, I can only think of a few, and they're not very major. Lenin's gov't immediately after the revolution looked to destroy the Orthodox church. They killed a bunch of priests to do so. Pol Pot's Khmer Rouge likewise does the same in Cambodia. The People's Republic of China - during the Cultural Revolution religious persicution reigned as it was viewed that religion was incompatible with marxist/leninist philosophy. French Revolution - The Terror, during this period many clergy were killed in the name of 'reason' as groups tried to push religion out of the country. Sapin - the Red Terror Anarchist and Communist groups during the civil war go out of their way to kill thousands in an attempt to wipe out religion in the country. I vaugly remember something in Mexico which almost led to a civil war, but could be wrong about that as well.
Sure, none of the gestures are as grand as some of the holy wars out there, but that's besides the point - people CAN do terrible things in the name of either one. It'd be foolish to think otherwise.
As for what he says to justify his statement, he kind of leaves out the point: it doesn't matter if they're done in the name of religion, atheism, or any other sort of ideology- these things happen and that's what matters. Often, the holy wars are only holy wars because that's the easiest way to motivate the populace* - they're really about something else entirely whether it be land, trade routes, cultural dominance, resources, or a grab for power. It doesn't matter if the Romans persicuted the Christians in the name of religion or if Stalin killed millions in the Ukraine in the name of the state - the end result is the same.
*This does not mean that the absence of religion would disable the leaders ability to motivate the people, history and human nature have shown us otherwise.