While the Tom Cruise episode was one of the biggest ways the show attacked the Church on the air, things got weird behind the scenes when long-time cast member Isaac Hayes parted ways with the show, reportedly over him having an issue with the show’s views of Scientology.
Yeah, I can’t imagine there’s any alternate dimension where anyone involved with Scientology would treat South Park with kid gloves.
(Here’s what Hayes’ son says about it all.)
Incidentally, the billboard that was sent to the aforementioned Church of Scientology in Los Angeles was likely the one that also visited a Whole Foods, a Hooters, a PF Changs and a KFC.