no post makes it onto the home page unless Eliezer endorses it; and he has to my knowledge never endorsed a post that disagreed with or questioned things he has said in the past.

Here's one example of a post that criticized Eliezer and others associated with SIAI but nevertheless got promoted to the home page: http://lesswrong.com/lw/2l8/existential_risk_and_public_relations/

I think there have been others, though I don't remember any specific ones off the top of my head.