|The CIA was created by the National Security Act of 1947. It replaced the (too-blandly named) wartime military Office of Strategic Services (OSS) and was deliberately concieved of as a civilian, non-law enforcement agency. From the act:
(d) HEAD OF THE CENTRAL INTELLIGENCE AGENCY. - In the Director's capacity as head of the Central Intelligence Agency, the Director shall -
(1) collect intelligence through human sources and by other appropriate means, except that the Agency shall have no police, subpoena, or law enforcement powers or internal security functions;
They were also concerned about miltiary officers being placed in charge of the Agency:
(c) MILITARY STATUS OF DIRECTOR AND DEPUTY DIRECTORS. -(1)(A) Not more than one of the individuals serving in the positions specified in subparagraph (B) may be a commissioned officer of the Armed Forces, whether in active or retired status.
Which required that at most one of the top 3 jobs at CIA could be a serving military officer. These limits are no relic, either, as they survived into the post-9/11 era in the Intelligence reforms of the 9/11 Commission, passed in 2004, which created the Director (and principal Deputy Director) of National Intelligence (DNI) and placed this limit:
''(c) MILITARY STATUS OF DIRECTOR OF NATIONAL INTELLIGENCE AND PRINCIPAL DEPUTY DIRECTOR OF NATIONAL INTELLIGENCE.-(1) Not more than one of the individuals serving in the positions specified in paragraph (2) may be a commissioned officer of the Armed Forces in active status.
In 2006, after Porter Goss resigned as head of the CIA, Bush appointed serving Air Force General Hayden to replace him. Most of the controvery about that appointment stemmed from Hayden's wire tapping activities as head of the NSA (which is always headed by a military officer). However, there was substantial concern (including from Republicans) that Hayden's military status made him a less suitable pick for CIA in the wake of the intelligence failures that led to the Iraq war.
"This is a civilian agency," said Sen. Dianne Feinstein, D-Calif. "And it's meant to be a civilian agency. So, you know, he might think about resigning his commission if he's going to do this," the senator, who sits on the Senate Intelligence Committee, told ABC News' "This Week With George Stephanopoulos."
In its 60-year history, the CIA has been run by a half dozen military men -- three while still on active duty -- but the Republican chairman of the House Intelligence Committee says it would be unwise to put a general in change now.
"He's the wrong person, the wrong place, at the wrong time," Rep. Peter Hoekstra R- Mich., said on "Fox News Sunday." "We should not have a military person leading a civilian agency at this time."
Hayden would be confirmed 78-15 (with Feinstein voting "yea" of course). One of those 15 nays was Dodd, who said of his vote (in part):
But today when the Senate voted on his nomination to be Director of the CIA , these two circumstances were significantly different. First, issues like the potentially illegal wiretapping of American citizens' phone lines by the National Security Agency--a program which General Hayden reportedly designed and ran--have come to light. And second, he will no longer be serving as a deputy but as head of one of our Nation's premier intelligence agencies--yet he is not resigning his commission as a uniformed officer. That raises the question of whether and to what degree he will be independent from decisions made at the Pentagon.
Some of my colleagues have insisted that Secretary of Defense Donald Rumsfeld will no longer be in the chain of command overseeing General Hayden in his position at the CIA . Certainly, there is precedent for uniformed officers serving as head of the CIA . However, when we look at this precedent we also have to realize that circumstances have changed. A not insignificant part of the reason that we invaded Iraq is because our Nation's intelligence was politicized, and because intelligence activities were manipulated to justify a predetermined conclusion--that Iraq had weapons of mass destruction.
The point of all this is that for 60 years, Congress has been very deliberate in trying to maintain a strong level of civilian control over the process and activities of intelligence gathering. This is a vital wall of seperation, due to the great power an agency like CIA can wield. I'm sure the example of the KGB and the domestic abuses of other totalitarian intelligence agencies was a large part of Congress' reasoning in keeping CIA in the realm of dirty civies. This isn't a minor matter, as from a pragmatic standpoint of intelligence gathering there is much to be said for consolidating all intelligence gathering into the military or FBI. FBI is technically civilian, but the powers of domestic federal law enforcement are dangerous enough without adding spying to the mix.
All of this was to both protect society from CIA, and to protect the CIA. CIA agents cannot be "ordered" to do anything in the legal sense, since they are mere civilian employees of a federal agency. They can quit and should do so when instructed to do things contrary to the Laws of War and numerous international treaties. These aren't scared 18 year old kids being intimidated into following Lt Calley into atrocity, nor do they go through months of indoctrination into a culture of rigid discipline as is done in the military. They are independent moral agents, and should not get any kind of pass for this.