JFK might be the one POTUS that actually tried to splinter the CIA into a thousand pieces, all it got him was a bullet to the head, a really loud warning to anyone else thinking of taking on the CIA.
If you needed any further evidence, they put Alan Dulles, CIA head that JFK fired but was still secretly running the agency from the shadows, on the panel of the "independent" investigation. If the CIA took out JFK it was Dulles who ordered it.