Broken Base: While the episode got good reviews, many considered it too dark for it's own good, most notably how brutal Chef's death was.
Fanon Discontinuity: Because Chef was such a well-loved character, many fans prefer to ignore this episode's existence for obvious reasons. Not helped by how needlessly brutal and disturbing Chef's death is.
Harsher in Hindsight: According to Isaac Hayes' son, Chef's "fruity little club" literally brainwashing and ruining "a cool guy" wasn't that much of an exaggeration. As it turned out, Hayes never intended to quit South Park in protest of "Trapped In The Closet," rather the Church took advantage of the fact that he'd just had a debilitating stroke and, in his absence, quit for him (not unlike what they'd done with Lisa McPherson)! "Trapped In The Closet" may have exposed what Scientologists actually believe, but this episode ended up (unintentionally) exposing what they do.
Heartwarming Moments: Kyle's eulogy for Chef is quite a touching moment, and really shows how much the kids cared about Chef.
Some Anvils Need to Be Dropped: The message regarding barely concealed Scientology metaphor of the Super Adventure Club is even blunter than their previous episode on the subject. The "Super Adventure Club" is a fruity club that ruined a "fun guy" and their beliefs are far more absurd and preposterous than the other major religions. Unlike Mormonism and other religions, Stone and Parker make it clear there is nothing redeeming or of value that the "Super Adventure Club" brings.
Tear Jerker: Again, Chef's death, and also his funeral.
Let's not forget the saddest use of the show's catchphrase.
Stan: Oh my god. They killed Chef. Kyle: You bastards... YOU BASTARDS!!!