"South Park" didn't ridicule Scientology, they just depicted with absolute accuracy what they believe, with a caption reading, "This is what Scientologists actually believe." No ridicule was necessary to make it hilarious.
We don't know for sure if Isaac Hayes really quit. According to Roger Friedman at Fox, he had a stroke in January, is incapable of writing any letters to anyone, and it's possible he may have been taken away from his necessary rehab by Scientology "minders," who could also be the source of that suspiciously thin-skinned and humorless resignation letter.
BTTT! And it was hilarious!