What I find funny is the fact that they didn't even make fun of aspies in the episode, and it wasn't really even about aspergers, at least not incredibly obviously. Either way, I don't see exactly what it is you think they're denying. And since when does south park appeal to the masses? I'll agree that this season hasn't been quite what I usually expect from Matt and Trey, but this particular episode was absolutely hilarious to me. There wasn't anything offensive about it whatsoever. If you were offended by it, I think you need to lighten up and learn to laugh at yourself once in a while. For one thing, the episode wasn't really even about you in the first place. For another, it's just a TV show made for the purpose of making people laugh.
If you think that Matt and Trey were portraying aspies in a negative light, making them appear to be complete fools, then you need to pay closer attention, and you totally miss the point of south park. There were only two aspie characters in that episode, and they were portrayed fairly accurately in the short time they were on the screen.