I haven't been watching all that closely, but I think I'm pretty well on Orac's side. I do think Maher deserves some amount of kudos for the balls it takes to release an anti-religion movie in the US. The problem: Maher's an anti-scientific crank and deserves major anti-kudos for all the tripe he spouts out.
When I didn't know much about the award, I thought it was just something like a PR award, and not quite so much to fuss about. I pretty much agreed with PZ's first post about it: Yeah, throw him a bone for the movie, but do everything (within reason) to put him in the hot seat for his crazy medical beliefs and such.
Then I found out about the science standards that were originally in place, and decided that no, I don't think The Crank deserves the award, and that it should be revoked. Not long after, I found out that they changed the award criteria for his sake, removing science as a standard. At that point, I performed a facepalm.
Many woos accuse us of valuing atheism/disbelief more than the truth, saying we wouldn't believe a scientific demonstration of gods. I think this whole scenario is an enactment of that stereotype: It sends a message that religion bashing is more important to us than science.
It doesn't help that my brother mentioned some dishonest tactics employed in Religulous. I never watched it, since I already had plenty of reason not to support The Crank, but I'm sure it won't take long for me to find out additional reasons to negate the kudos given for that movie.