Why in the world should we care about metaphysical entities in people's heads to the point of changing our ethical judgements on them?
Following the insights of Max Stirner, I would go still further and claim that the difference is not between belief systems that involve metaphysical entities and those that don't, but merely between different kinds of metaphysical entities. This means that the issue at hand is whether the antropomorphic quality of these entities is by itself such an important difference for the worse.
The really scary thing is that humans seem incapable of establishing a workable system of Schelling points that would be capable of serving as the basis for organized society, and which wouldn't base its Schelling points on some kind of shared metaphysical fictions. An objective evaluation of different belief systems that are capable of filling this role would be a fascinating project. (Unfortunately, it would also be a project of immense difficulty, not just because of the sheer complexity of the problem, but also because all sorts of biases would interfere with it -- not least since it would likely make the current reigning ideologies look quite bad in comparison on at least some important metrics.)
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?