According to The Superficial, Isaac Hayes actually doesn't have a problem with the way Trey and Matt handled the Scientology episode. They even have a clip from of an interview that Hayes gave in December where he said he was okay with it.
It turns out that the Church of Scientology are the ones who wrote the press release over a week ago which said:
"There is a place in this world for satire, but there is a time when satire ends and intolerance and bigotry towards religious beliefs of others begins," the soul legend said. "Religious beliefs are sacred to people and at all times should be respected and honored. As a civil rights activist of the past 40 years, I cannot support a show that disrespects those beliefs and practices."
Turns out that it was Christina Kimball, a fashion editor for Craig Taylor and fellow Scientologist, who sent out the release, or so says Page Six and foxnews.com. According to them, Hayes, in fact, loves South Park and needs it for his new baby that's on the way. He only left the show after suffering a stroke (ouch).