Update: Stone and Parker comment semi-obliquely on the situation in the South Park season premier.
I recently mentioned Isaac Hayes quitting South Park due to a Scientology-mocking episode and Comedy Central pulling the episode due to Tom Cruise threatening not to publicize for M:I-3. Now, it seem both Paramount and a Cruise representative have issued statements saying Tom Cruise did not threaten to withhold publicity for M:I-3.
Comedy Central said it replaced the episodes with ones prominently featuring Chef because "we wanted to give Chef an appropriate tribute by airing two episodes he is most known for." That sounds quite plausible to me, actually, and maybe they were trying to flatter him and win him back?
However, it also seems that Hayes' decision to leave the show was a surprise to his friends. In fact, in a January 2006 interview, he was asked about the episode. He responded:
Well, I talked to Matt and Trey about that. They didn't let me know until it was done. I said, "Guys, you have it all wrong. We're not like that. I know that's your thing, but get your information correct, because somebody might believe that shit, you know?" But I understand what they're doing. I told them to take a couple of Scientology courses, and understand what we do. [Laughs.]
That doesn't sound so bitter. So cue Church of Scientology pressure conspiracy theories. :)
I got those links and info from this blog:scanners post.