This argument fails several ways. First as history. Some of the atrocities happened without central organization -- e.g., Islamic fundamentalists aren't all part of any one organization, although they've created a variety of more or less hierarchical organizations; the displacement of the Indians (which had essentially nothing to do with religion except as a stock of rationalizations for things people would have done anyway) -- and all the others had important elements of individual initiative.
(I must say I found it amusing that you concede that the crimes against humanity committed by atheist states weren't solely the fault of religion. When you start saying things like that, you've spent much too long seeing arguments as weapons to be used on behalf of "your side".)
Second, it refutes a position nobody holds. No religionist believes in a flavor of God-implanted moral sense strong enough to overcome all the various temptations to behave immorally; usually they believe quite the opposite, that it was mostly or totally broken by some sort of Fall. If you find yourself triumphantly refuting a view that cannot in any case survive contact with ordinarily accessible reality, you're probably dealing with strawmen.

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There is another kind of single point of moral failure besides social structures. It is possible for people to structure their beliefs in such a way that adding a single false belief breaks their entire moral system. For example, if someone truly believes that all morality comes from God, then their behavior will change drastically for the worse if they come to wrongly believe that:
There are plenty of cases where people have come to believe such things, and turned evil because of it. If you model people as having a bunch of beliefs that they received from their parents and from observation, then throw a few randomly-generated or maliciously-optimized beliefs on top, then one way to judge the quality of a belief system is by the amount of harm that the extra, false beliefs can do. If someone attaches all their moral beliefs to a single concept like God, then a single new false belief involving that concept can turn them evil. On the other hand, someone who knows a bunch of moral rules and believes them to be individually justified (preferrably justified in multiple ways) can't have that happen.
Note that not all theistic belief systems have this problem, and major religions have safeguards (albeit imperfect ones) against certain morality-breaking falsehoods. There are also plenty of non-theistic belief systems which have the same problem.
If I rationalize it to my own satisfaction and/or just don't care, it's indistinguishable from being good.
With the added nastiness of not actually being wrong. Except that if you ever notice yourself thinking this the gig is already up.