I'm afraid you are mistaken. Thompson did plenty of Klintoon bashing. I'll try to find some links for you.
Hmmm. I remember just one critique of Clinton, in 1992 in RS, but his political writing disappeared, at least from Rolling Stone, after that. I just guessed that someone on the high Left "got" to him. He wrote about thoroughbred racing or pollo or something.
I'd like to read his critiques of the Clinton cabal. Looking forward to it.