Hmmm, interesting question. If you were to ask about conservatives versus progressives in general, I would say yes: The fact that bible-thumping Christians are far more likely to be conservative alone is enough to skew the average downwards. But the people who partake in the Less Wrong census and identify as conservative are a very different demographic, most likely.
All in all, I would have to say yes: I think it is much more likely that those 3% of Less Wrongers identify as conservatives because they are the kind of people who fail to apply rationality to their politics (and therefore have lower IQ) than it is that they identify as conservative because they are free and independent thinkers who are willing to go against the consensus opinion on this website (higher IQ).
Care to give odds? There is a narrow opportunity for betting (until Yvain releases results).
A long blog post explains why the author, a feminist, is not comfortable with the rationalist community despite thinking it is "super cool and interesting". It's directed specifically at Yvain, but it's probably general enough to be of some interest here.
http://apophemi.wordpress.com/2014/01/04/why-im-not-on-the-rationalist-masterlist/
I'm not sure if I can summarize this fairly but the main thrust seems to be that we are overly willing to entertain offensive/taboo/hurtful ideas and this drives off many types of people. Here's a quote:
The author perceives a link between LW type open discourse and danger to minority groups. I'm not sure whether that's true or not. Take race. Many LWers are willing to entertain ideas about the existence and possible importance of average group differences in psychological traits. So, maybe LWers are racists. But they're racists who continually obsess over optimizing their philanthropic contributions to African charities. So, maybe not racists in a dangerous way?
An overly rosy view, perhaps, and I don't want to deny the reality of the blogger's experience. Clearly, the person is intelligent and attracted to some aspects of LW discourse while turned off by other aspects.