I have been thinking about this, not a helluva lot you understand just thinking.
I have come to the conclusion that Hayes isn't leaving because of the episode that slagged off scientology.
I think he is leaving because the South Parks Guys took so long to actually including scientology in an episode.

The Episode "Super Best Friends" covered quite a bit of turf when it came to Religion and beliefs.
It had Jesus, *Muhammed*, Krishna, Joseph Smith, Lao Tsu and Moses...The Super Best Friends. (* that got me thinking a bit actually)

So I think that Haynes and his lot are just p'd off that it took a few years before they got the nod.
Hayes didn't have any problem cashing the check for his work on the show through the years as one of it's Writers said.
So I think it is more that South Park didn't focus enough on Scientology rather than it focused on it at all:)
Hayes leaving won't change the show one bit. I think Chef will stay and someone else will do the voice...if Chef does go though it will be way OTT for sure.
They are running the Scientology episode just before the start of new Season I think...just to rub it in.

Just a thought I wanted to share with you all before my bedtime...