I don't think it's really attacking Hayes so much as Scientology. They really made a point to show that all the South Park characters really cared about Chef, Cartman crying when Chef left, etc. Besides, re: Scientology/child molestation thing; don't they usually do exaggerated logic extensions in their other stuff anyway? Like Christopher Reeve sucking on dead fetuses to gain super strength. Or TEAM AMERICA where Michael Moore is a suicide bomber, among other things. Using a NAMBLA type group as an analogue to make fun of Scientology further would be par for the course.
Actually he did once. The older episode where Cartman gets amnesia and thinks he's a Vietnamese prostitute. When he gets thrown off the bull and they think he's dead. Kenny says "Oh my god! They killed Cartman!" They just showed that one a little while back.
I just find it funny that he gets offended by people making fun of his religion, and quits his very well paying job, when Scientology (though a ligeitiment religion in my book) is possibly one of the most often ridiculed religions. You'd think he'd be used to it from other people and wuld've expected it given the nature of South Park.