After having read that article, I'd still say that what we saw in the episode was intentional. What probably happened was, Trey and Matt pitched their conceptual idea of the episode (including the showing of Muhammad) to CC, which was turned down, so they probably did it in such a way that let everyone know that CC hadn't allowed it.
Let's say that episode aired uncensored. We would have seen Muhammad give Peter the helmet, right? Then they would have showed that American guy saying "oh, that wasn't so bad" or whatever it was. That wouldn't have been funny at all. It was clearly intentionally meant to be that way, imo. They probably said "ok, CC won't let us show Muhammad, how can we write the episode to get around this?" They wouldn't just air the episode with a small section censored, they'd pull the entire episode, no?