It's taken as read inside the Beltway that the CIA had JFK murdered because he was about to seriously curtail their activities and have a full examination of covert action. The debate is over which faction(s) were directly involved and whether the other factions signed off on it or just covered up afterwards. The actual math is insanely complex and I am in no way an expert. But plenty of books have been written.
It was institutional self-defense. The CI establishment has done a lot of extraordinary things over the years. Some have been frankly amazing. Some have been borderline coup. And, once, it was an actual coup.
The Church Commission would perhaps have cut them back except for what happened subsequently in American history.
It's awful, but it's true. America lost its cherry in 1963. It's happened to every other empire, and it happened to us. Since then, we've just been making do and trying to minimize the damage.