Geez, no kidding. I loved Team America but the first movie was a little over the top for me.
That was a pretty stupid end of South Park...but I understand what they were doing.
Issac Hayes (Chef's voice) left SP because he's a member of that cult, Scientology and he was mad because SP mocked it.
Hence..."we shouldn't be mad at chef for leaving, we should be bad at that sick gay club for brainwashing him..."