Your line here is a reaction to statement of a fact, variously phrased, that religion has been the motive for the killing of a great many people down the course of human history. Being a religious person, and one who conflates 'religion' with 'good and moral', this troubles you, particularly when it is stated by persons who do not believe there is any Deity, and that all religion is therefore fraud and lies. So you attempt to throw the charge back at them, and claim atheism is the motive for mass murder on a scale that dwarfs killing done from religious motives. In doing this, you engage in a variety of distortions of meaning and shadings of fact. They are pretty obvious, but worth stating openly, as you persist in them so energetically; room must be left for the possibility you really are not aware of what you are doing.

When people say religion has been the motive for killing a great many people, they do not mean that people who hold religious beliefs have killed a great many people, from whatever motive: that would be a wholly unremarkable observation, and hardly worth the typing out. They mean that people have killed other people from motives of religious belief, killed to suppress a dissident sect in their society, or to extend the range of dominion their religion exercises, or killed to enforce a code of behavior inherent to their religion, or killed as matter of religious ritual or rite. And in fact a tremendous number of people have been killed down the course of human history over these directly religious motivations. These are killings which, it could be fairly claimed, would not have taken place without religion, or more precisely, without the religious beliefs the killers felt directed them to kill others as a matter of sacred duty.

When you say in response, 'well, atheists have killed lots and lots of people,' you fail absolutely to tie this into any element of atheist doctrine or belief that requires such killing, and so do not actually mirror the statement you are attempting to defend against, that religion has been the motive for a great deal of killing, that a great deal of killing has owed to the killers subscribing to a religious belief the killing they engaged in was required by their Deity, by their holy law. Since there really is no 'doctrine' of atheism beyond the statement that there is no Deity, it is hard to see how you could tie killings by atheists into some atheist doctrine, in the way that, say, the persecution of heretics or wars of conversion can be tied directly to items of religious doctrine, or the killing of persons on a high altar by priests, or in funerary rites, can be tied directly to requirements of religious ritual or enforcement of a sacred code.

Adopting the standard you wish to apply to killing by atheists, you would have to accept that every killing throughout human history by a person who held a religious belief was a killing that should be charged up to the account of religion, and that it would owe to religion, regardless of its actual motivation. This would chalk just about every death from human agency since we first appeared as a species to the account of religion; indeed, it would include a great many of the killings you ascribe to atheism on religion's side of the ledger, since the actual agents of death, the guards in the camps, the personnel of the squads that carted away the grain, were as a matter of practical fact shot through with persons who retained religious beliefs; even if they were acting on the order of an atheist, they were the ones actually doing the killing, after all.