That may well be the case DaveM but Clinton's 'Schwantz' control was a weakness to be potentially exploited. 'conspiracy theories' have been given a bad name and most folk lump them all together alongside way out there theories such as Elvis lives and works at the local grocery store. But conspiracies DO exist at high levels by people in power. Whether it was Bush and Blair conspiring to invade Iraq come what may and spying on 'allies' such as bugging the Spanish prime minister to ensure he remained supportive, to the most recent case of traders colluding together to fix the foreign exchange rates. Don't ever under estimate intelligence agencies, remember you only ever hear about their failures. (Generally speaking). If you have a president who's doing something you don't want him to do, why not find 'leverage' on him? Find a distraction...
JFK sacked Dulles, he wanted to smash the CIA into a thousand pieces and scatter them to the four winds...
Going off subject, when you have a nation who spends more on defence than the rest of the world combined, whose economy is dominated by a military industrial complex, an organisation like the CIA is the 'brains' of that military industrial complex. This apparatus needs an enemy to exist, the cold war provided stability, we had to keep up with the Soviets, now that's finished...every time you see the CIA budget come under threat, a new enemy arises...The CIA and the military industrial complex are not going to let a short term occupant of the White House change them or shut them down, they just help maintain an illusion of power for any POTUS. If a POTUS crosses that line, then well...
So if a POTUS gets wind the CIA or any other secretive group within the U.S, is up to something they shouldn't be doing, or have something he thinks he should see, these same covert, secretive groups are going to defend themselves. Let's face it, they are in the the profession of taking on the best of foreign intelligence services anyway, what hope does a POTUS have of taking them on?