No one likes to be mocked, but Tom Cruise seems to be making a religion of it with the dustup over the way Scientology is treated in the animated series “South Park.” In November, an episode of the Comedy Central show hit the Scientologists with its trademark unrestrained satire. Mr. Cruise, one of the church’s members, reportedly wanted repeats of the episode, “Trapped in the Closet,” pulled from circulation.

Viacom – the parent company of Comedy Central – obliged. Mr. Cruise is the star of an upcoming movie, “Mission: Impossible III,” made by another Viacom unit, Paramount Pictures. The star is said to have balked at promoting the movie, which perhaps explains why “Trapped in the Closet” was removed from its March 15 slot.

Last Wednesday, Comedy Central responded by airing “The Return of Chef,” which was devoted to an obvious (and hilarious) send-up of the church in question. Even though the group was the butt of the joke, the net result of the affair made clear that in the entertainment industry, Scientology has juice. Mainstream religions: nada.

Consider how Comedy Central handled the December “Bloody Mary” episode, in which a bleeding Virgin Mary was a source of comedy. Catholic groups, including the Catholic League for Religious and Civil Rights, wanted the episode pulled from repeats. It was removed from a year-end “South Park” marathon in deference to the Christmas holidays. But, as the New York Post reported, the network then sent out an e-mail, in response to angry viewers’ complaints. The note stated that the religious groups had not won a victory.

The episode did “air in every one of ‘South Park’s’ normally scheduled repeat timeslots.”

It had not been permanently pulled, Comedy Central executives wrote, nor would it be kept out of DVD releases. The e-mail further stated: “We appreciate your concerns about the potential influences of outside special interest groups on the media and entertainment industries, and particularly Comedy Central.” But, the executives said: “As satirists, we believe that it is our First Amendment right to poke fun at any and all people, groups, organizations and religions and we will continue to defend that right. Our goal is to make people laugh, and perhaps if we’re lucky, even make them think in the process.”

This righteous theory of comedy was certainly put into practice for “The Return of Chef.” But where is that tough talk and ringing endorsement of the First Amendment now? Is “Trapped in the Closet” ever coming back? It certainly looks as if Mr. Cruise and the Church of Scientology got what they wanted. Though they did not escape unscathed, the Scientologists won a battle that the Catholics could not. The episode may someday rise again, but for the moment, it is gone.

Which brings the Scientologists’s unique position to the fore. Forget, say, Christian evangelical boycotts or the protestations of the Anti-Defamation League. They pale in comparison to the force of one aging male pinup, who has never won an Academy Award but happens to believe in the right stuff.

Isaac Hayes, who was the voice of the recurring character Chef has since quit the show. There has been some debate over the reasons for his departure, but Mr. Hayes is a Scientologist, and that could be the cause. “South Park” can go on without him, as creators Trey Parker and Matt Stone demonstrated last week. But as Mr. Stone has mentioned, Mr. Hayes has been on a show that mocked any and all religions for some time without any complaint from him. Until perhaps now.

While Viacom missed an opportunity to stand up for free speech, it also missed an even bigger opportunity: to be a delightfully Cruise-free zone. Would Mr. Cruise’s absence at the premieres of “Mission: Impossible III” really have made any difference at the box office? Doubtful. Mr. Cruise has embarrassed himself so publicly in the last year on “Oprah” (regarding his squeeze Katie Holmes) and with Matt Lauer (regarding antidepressant prescription drugs) that it’s hard to see him as an asset rather than a liability.

What a delicious moment it would have been if Viacom had pulled the red carpet out from under Mr. Cruise. Talk about corporate responsibility. The “South Park” demographic would have eaten it up – and maybe even bothered to see the third entry in the “Mission: Impossible” franchise. Instead, a multibillion-dollar company is letting an actor lead it around by the nose. It’s the ultimate reversal of the studio system.

And it raises a larger cultural question far beyond the toothy grin of Ms. Holmes’s boyfriend. Does a schism like this dilute our perceptions of actual religious bigotry? Mr. Cruise’s objection to the cartoon was raised in the wake of a news cycle in which Muslims were rioting over political cartoons about Islam. What does that mean for the Anti-Defamation League’s campaign against anti-Jewish cartoons in the Arab press? To reduce these three matters to a common denominator would be its own kind of satire, but that’s not to say it won’t happen.

pcatton@nysun.com