Ultimate Axiom, you bring a much-needed sense of clear-headed analysis to this interesting topic. I like the way you show that both "sides" - so to speak - of the argument are inclined to simplify the issue of athiesm versus theism is more/less inclined to engage in "mass murder". Your appraisal is sobering and considered.
Your comments about nationalism are on a par with those of Emile Durkheim (the sociologist who lived in the 1820s - 1830s) who recognized that religiosity was symbolic of devotion to one's (national) group "writ large". He wrote extensively about the ways in which human beliefs in the "divine" have grown out of a need to look up to and follow and protect one's group - but that over time the overtly initiating need to belong in a group becomes overtaken by symbolic beliefs about an all-powerful "god" - who really just stands for the group "writ large".
Group membership (i.e., nationalism) is often the major force behind people's behavior - and that behavior doesn't need to be religiously motivated but that in the 19th century is was to a degree never seen in history before (a function of a large world population among whom were more nations who were identified in one way or another with religion. But as you point out, there were also examples of nonreligious (and athiestic) leaders who were as adept at whipping up nationalistic identity - the core of what underlies egregious acts on a mass scale.