Just got to watching the episode this morning, and I have to say, I honestly think Matt and Trey had to be in on the censoring thing. I mean, there's probably real graphics behind everything (as DrEvil is proving), but something about the whole episode seemed a little off. It felt like they were actually trying to say Muhammad a lot more often than would be necessary, for instance, and having three characters at the end make long speeches seemed odd. Plus, Stan's (or Kyle, never remember which is which) "yeah!" right after the three speeches just fits all too well with the censor bleeps.
I doubt Matt and Trey wanted it to be censored, but I'll bet they were given the word that it would be early on, so they decided to throw a few nods to the censorship in there. I got a strong feeling watching it that this wasn't a totally last minute censor job like they say it was. Plus, IMO bleeping out half the episode makes the radical islamic censorship look worse than it ever could have otherwise, which you know would be right up their alley.