This episode's mocking of Scientology supposedly did not sit well with Isaac Hayes (Chef), a practicing Scientologist. Co-creator Matt Stone stated that Hayes voiced his concerns to him, and that it was clear that he had been pressured into requesting the episode to be canceled (a moot point, as it had already been broadcast by then). Four months later, a statement was issued in Hayes' name that he had left the show. However, after Hayes' death, his son stated that Hayes had suffered a stroke that left him in no condition to quit on his own. Supposedly, one of Hayes' close confidants (all Scientologists as well) had made the statement on Hayes' behalf.
Jenna Miscavige Hill, the daughter of the chairman of the Church of Scientology, first learned about the Xenu story from watching this episode. She left the Church of Scientology shortly after and has become an outspoken critic of the organization.
This episode was pulled from airing in the UK and as a repeat on Comedy Central because of Tom Cruise's objections.
Stan's final lines "Sue me, I dare you!" was an actual in-show threat by the creators who are daring Scientologists to sue them for mocking their 'religion.' The Church of Scientology has a well-known history of suing its critics, including lawsuits in the UK (thus the line "We'll sue you in England!"). Defamation laws in England & Wales are extremely plaintiff-friendly: once a plaintiff has proven that a statement could potentially affect his or her reputation, the defendant must prove the truth of the claim on a balance of probabilities.
In keeping with the running gag of "daring" the Church of Scientology to sue them, at the end of the episode when the credits began to roll, all the names of the people who helped create South Park are replaced with either "John Smith" or "Jane Smith." A humourous attempt at hiding the names of all the people involved with the show immediately following the last scene of the episode where one of the characters is literally yelling at the "viewer" to "Go ahead! I dare you to sue me!"