I think it was the, "he just had a stroke" part that made him know that Isaac didn't make the decision.

A full decade after Hayes quit South Park, his son, Isaac Hayes III, told The Hollywood Reporter that Hayes had suffered a stroke in January 2006 before he quit, and that he didn’t leave the show. “Isaac Hayes did not quit South Park; someone quit South Park for him,” Hayes III maintained. He explained that the initial stroke took away his father’s ability to speak as well as some cognitive comprehension. “He was in no position to resign under his own knowledge,” Hayes III continued. “At the time, everybody around my father was involved in Scientology — his assistants, the core group of people. So someone quit South Park on Isaac Hayes’ behalf. We don’t know who.”