What was really funny was, they didn't lie or exaggerate about Scientology beliefs, from personality tests, auditing and e-maters to Xenu and OT's (note the disclaimer "This is what Scientologists actually believe" during Stan's briefing, no joke there). Everything from Xenu, to the "OT" levels and nobody has reached OT 9 (their current program ends at OT 8, but theoretically goes to OT 15 and only L. Ron ever went beyond OT 8 so far, and 9 will supposedly only be released once Scientology is a major world religion).
Also notice that Chef wasn't in the episode at all? Probably because Issac Hayes is a prominent Scientologist.
They made a vague parody of Scientology back at "Super Best Friends" with Blainetology, and with Issac Hayes in the cast I thought they'd never actually make a direct satire on the CoS, but they did it, and they did it well.
They got just about every "out of the closet" joke they could possibly make with Tom Cruise, which was just really funny. Predictable and silly, but still worthy of some strong laughs.
It was also funny how they were practically daring the CoS to sue them (as for factual tenets of their faith, the Fishman Affadavit already backs everything they said up), only the end where the leader tells Stan it's really all a scam would be any place to go to, but this is the same show that depicted the Catholic Church as being lead by a giant spider and is a worldwide conspiracy of priests to molest children, Sally Struthers as a Hutt who really keeps food away from the needy, Stevie Nicks is a goat, and openly mocked the origins of the Mormon church (including background chanting over their founding story of "dumb dumb dumb"), and I'm sure they'd love the publicity of a big lawsuit if the CoS sued them (and getting them to admit in court their beliefs are as listed on the show, and that they weren't making these things up). I'm mildly surprised they didn't depict the head of the CoS as David Miscavige, but maybe depicting the actual leader of Scientology as the person saying it's all a scam might have been a legal bridge too far.