Just a little speculation on why the speeches at the end were also bleeped, even though they don't mention Mohammed.
We know that the speeches were going to be about fear and intimidation. I think Kyle, Jesus, and Santa were going to make the point that no one is immune to ridicule. Not celebrities with high-priced lawyers, not gingers with explosives, and not Mohammed.
And then, after Stan says yeah, we would see a quick shot of the censor bar around Mohammed vanishing, just like Tom Cruise's bar. Mohammed would be clearly visible. He wouldn't be doing anything funny, or saying anything at all. He would just be standing there, lookin' normal. And we would only see him for a second.
Of course, if Comedy Central isn't going to allow his name to be spoken, they certainly aren't going to allow him to be shown. So that part of the episode was cut out. But the speeches just before it don't make any sense without that shot. So Comedy Central bleeped all the speeches and tried to pass it off as a joke about their own censorship.
Again, that's just a hunch. I have nothing to back any of that up. Just a gut feeling.