I'm not sure the "pulling" of the Scientology episode (
Trapped in the Closet) was quite the same as the pulling of the "stigmata" episode (
Bloody Mary). My impression is that Bloody Mary was pulled from future broadcasts specifically because of protests from Catholics (the producers/CC have said as much) whereas Trapped in the Closet's missing repeat the same week of Hayes' departure was just to let temperatures cool down for a bit. I don't recall reading anything about an official protest over TitC, other than rumors of Tom Cruise's alleged refusal to promote Mission Impossible 3 if it wasn't pulled. Do I think Cruise is capable of such shenanigans? Hell yes! But until I hear something from Matt & Trey confirming the rumors, I'm not going to jump to that conclusion.