Believing in God may be "below the sanity waterline", but there are plenty of other ways to have crazy beliefs for the wrong reasons (anything other than "because as far as I can tell, it's true") while being an atheist - about about science, about themselves, about politics, about morality ...

I think the "politics is the mind killer" policy is a bit of an avowal that the people here are fully capable of irrationality, and that it's more productive to just avoid the subject.

If OB/LW had started a few centuries ago, maybe the policy would have been "religion is the mind killer", with a general recommendation to not talk about religion less people get excited. Hopefully in a few centuries politics may not be the mind killer either.