As a devout Christian, I enjoy that show's jabs at religion every time. Not all Christians have Mr. Twig up their ass when it comes to religious humor when it speaks the truth. Monty Python cured us of that in '79. Jews rip on themselves all the time (Seinfeld, The Hebrew Hammer, History of the World, Richard Belzer's stand-up, the list goes on) and hardly anybody from their faith gets their knickers in a twist.
I'm curious as to why it took Isaac Hayes four months to denounce the episode. Perhaps he's feeling the pressure from the higher-ups in his cult? Because you CAN'T associate with ANYBODY who badmouths Scientology if you're in the club.
For those who haven't seen the episode, find it and watch it. Then spend a few days googling the crazy crap South Park showed us and you'll see that it's pretty much all true. ... and is even worse than what was covered. Perhaps the best debunking site is Operation Clambake. You'll never see Tom Cruise, Kirstie Alley, John Travolta or any of those pricks the same way again. Maybe it's just the Thetans talking, but I think L. Ron is laughing right now at all of them from his cozy room in Hell, where his stacks and stacks of cash incinerated upon arrival.