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).