Yeah, the whole thing got a little strange...
I only catch the Colbert Report on-and-off, but watched a few after the "controversy" started. His bits with it were actually pretty funny.
I still think they should go with Serenity. Colbert says if they don't name it after him, he'll take over as space's evil overlord (or some such). I say, let him. I welcome our new comedic overlord.