One comment: the atheist friends who judge me on associating with Christians are, for the most part, not professed rationalists. I doubt their belief systems are any more self-consistent than those of my religious friends; they just don't happen to contain God. I certainly don't think it should be part of any rationalist belief system to judge! Just that it happens to me (and it also happens to me from my brother, who DOES claim to be a rationalist and reads LessWrong) and that I find it unpleasant.

I like how you make the distinction between judging people based on the friends, and limiting contact with them based on your judgement. I do the first (probably a bit less than most people, but that has more to do with the fact that I have an "agreeable" personality than anything else) but I try very hard not to do the latter, and hate it when people (mostly coming from the atheist side) try to ask that of me.