Just brainstorming for a new counter-argument. Perhaps someone can use better wording and expand on this idea...
A few years ago I got into a debate with a Christian. He ended by saying that Atheists killed more people throughout history.
In the debate, the theist "stacked the bodies"/tallied the amount of people that died under Stalin, Pol Pot, and Mao Zedong. I don't remember the count right now, but it was extremely high. Anyway, I responded back by tallying the amount of deaths as a result from theists (+80 Million deaths under Hitler's 3rd Reich, +80 Million Hindus killed by Muslims, etc.).
The theist's response will be "those weren't true Christians" or "they didn't kill those people because of religion. That being said, some of those deaths which are attributed to those atheists were not directly carried out by them (starvation under Mao Zedong's rule). So in this case, the murders were not a result of "atheism" (though it's not a ism). Basically, it's a special pleading fallacy when the Christian refuses to acknowledge the deaths as a result of theists, while accepting the deaths which was not a result from "atheism".
And also, if we were to stack the bodies from the beginning of civilizations until today, and count the murders of every single day from then to now, we would see that most of the murders have been carried out by theists, since theists make up the majority of the population. We could tally up how many theists are in jail for murder.
Christians will say that these theists weren't acting in accordance with religion, and we'll say that atheists weren't acting in accordance with atheism, and when we arrive to the total number of deaths as a result from theists, we used the theist's logic.
Of course it becomes more complicated when a Christian stack the bodies of murders committed by all non-Christians (including Muslims, Hindus, Shinto, Norse, etc) vs Christians. So in order to find out, I guess I'll have to do the research again.
"So far, nobody knows the mysteries that lies behind the formation of the universe. But at least I don't make up an answer, rationalize it, call it god, and then pretend to know." - Raby