first, you put a lot of emphasis on chaltab's comment that his family should disown him. now, in my forum "experience", i've noticed that people tend to exaggerate when they feel strongly about something, so i do not think that he meant it in the sense that if he could sell his soul to the devil he would wish for Hayes' family to disown him. i could be wrong though, it's just the impression i got.
second, well it is blatant hypocrisy on Hayes' part, even if it's true all the facts are not known. South Park is a show that satirises EVERYTHING. not only religions, but also celebrities, politicians, ways of life etc. Hayes has worked long enough for the show to know this. Many many many groups have been offended by things South Park stated, Hayes is not the first one.
BUT I agree when you say that he might have been blackmailed into doing it. Still, he could just have quit the show, giving other reasons maybe. and if scientology demanded he should say openly why, then he could have toned his comment down.
I think this discussion maybe started to focus too much on the cult, and not on the actual news, I understand that is what makes you angry.
Although, I have to say that it IS weird that he waited a couple of months to resign...I don't know what to make of that, maybe his scientologist friends started to ostracise him and make him feel guilty.