This smacks pretty strongly to me of undiscriminating skepticism. If you refuse to entertain the notion of a relevant difference between throwing people into Mount Fuji (not that there's a lot to throw someone into)because you believe that a god demands it and throwing people into Mount Fuji out of a sense of retribution, are you going to entertain the notion of a difference between campaigning to stop an AI project because they always turn out badly in movies, and campaigning to stop it because you've got strong reason to believe it will FOOM into an Unfriendly AI? How about discriminating between people who want to be mummified so they'll be whole in the afterlife, and people who want to be cryonically frozen? Or between the Rapture and the Singularity?
An action may be the same regardless of what motivated it, but different beliefs have different implications. They will change according to different evidence or reasoning, or when different belief nodes are switched (for example, a moderate Muslim's actions may be changed by being convinced that the original intent captured in the Koran was for Islam to be spread by the sword, in a way that a non-Muslim's absolutely won't be.) And if you can't discriminate between strange seeming actions by the actual reasons that motivated them, then you're just going to end up judging according to your own adopted memes and cultural norms.
But if we make this one trivial change, turning Nazism into Thorism and making it a "religion," which as we've seen need not change the magnitude or details of Nazi crimes at all, the acts of the Allies are a blatant act of religious intolerance.
Aren't we supposed to respect other faiths?
It's certainly convenient to do so when you can't discriminate between differing beliefs on the basis of evidence. If you default to not respecting complex webs of belief unsupported by evidence, the problem goes away. But it certainly doesn't require you to not recognize a subcategory of belief webs as "religious".
I've recently run across this 2007 post on the blog Unqualified Reservations (archive best read here). It is written by Mencious Moldbug, who is probably familiar to some Overcoming Bias and Lesswrong readers. He is a erudite, controversial and most of all contrarian social critic and writer. In 2010 he debated Robin Hanson on the subject of Futarchy.
Violating Godwin's law to breach the fence between religion and ideology to see what cognitive dissonances we can dredge up is old hat for us LWers (A Parable On Obsolete Ideologies 2009 by Yvain).
I hope you can now see reason I've picked a partially misleading title, since I think Moldbug makes a pretty convincing argument that belief in "religion" may be considered harmful even for atheists, let alone those of us who aspire to refine rationality.
In such a model questions like "is the Church of Scientology a religion?" dissolve rapidly. Whether something should be tax exempt because it is "really" a "religion" or "a church" is a legal question of importance only to activists trying to challenge law and lawyers, that shouldn't change our ethical intuitions or cause us to try to imagine a sea or play up rather minor geographical features, to separate the continents of Religion and Ideology in our maps of reality.
Every single proposed mechanism for the retention and spread of religion from convenient curiosity stoppers, indoctrination of youth, to tribal identity markers hold for ideology just as strongly as for religion. Even seemingly very specific memetic adaptations like "God of the gaps", seem to arise in various non-theistic ideologies. Maybe similar adaptations arise because it is the same niche?
Thinking about the implications of such a hypothesis, atheism for one additional god is a rather easy step of rationality to take. Very few people believe in the great Juju or Zeus. Adding YHWH to the list isn't that much of a stretch, for those fortunate enough to be educated and living in most of the West.
But how hard is it for someone to question, in a unbiased fashion, such gods and holy words such as say Democracy?