Matt and Trey released a statement today on southpark studios.com
A Statement from Matt and Trey
In the 14 years we've been doing South Park we have never done a show that we couldn't stand behind. We delivered our version of the show to Comedy Central and they made a determination to alter the episode. It wasn't some meta-joke on our part. Comedy Central added the bleeps. In fact, Kyle's customary final speech was about intimidation and fear. It didn't mention Muhammad at all but it got bleeped too. We'll be back next week with a whole new show about something completely different and we'll see what happens to it.
I can't wait for their response next week...