More importantly, concerning Less Wrong itself, should we try to distance ourselves from atheism and anti-religiousness as such? Is this baggage too inconvenient, or is it too much a part of what we stand for?

I think it would be a mistake to distance ourselves from these. A tool the religious use is to pretend disagreement with them is crazy. Countering this idea is CENTRAL to rationality. Being afraid of being sent to hell for eternity is no more "evidence" that god exists than is being afraid of tigers evidence that there is one in your back yard. A central reason why the scientific method has succeeded so remarkably is that it automatically enforces the rule that just because you want something to be true doesn't make it true, and indeed is not even evidence for its truth. If anything, it is evidence that you need to be more skeptical of the idea if you want to get it right to counteract your own bias.

In my opinion, the best advantages rationality can gain is a totally reasonable intelligent well spoken blond woman wearing sleeveless dresses smiling and explaining with devastating clarity just how much sense atheism makes. The reason this makes the mullahs want to spit at her and kill her is because it is a threat to what they are selling, which is precisely why rationalists should keep doing it.