I don't know if this is an official or unofficial statement, but what I have from the Church is "South Park aired an episode on Scientology last year that erroneously portrayed our 'religious beliefs' while mocking them. South Park is not going to change anyone's mind about anything it's a cartoon."
Personally, I was pretty bummed by the episode, but I had long ago stopped watching South Park. For the first several seasons I was a big fan. I thought the movie and the message from it was great. I was not particularly a big fan of their ripping on religion at any point, even their "Spirit of Christmas" bootleg.
I know Matt and Trey are equal opportunity offenders, but they used to make good points, now they just try to piss people off. That's my opinion anyway.