Prator: The CIA is an organization with a short history of being run by people who are
A. Zealous to a fault in their prosecution of Communism,
B. Paranoid to the point of insanity (I'm looking at you, J.J. Angleton!),
C. More focused on personal politics than the world issues they influence (more common when politicians and not soldiers are placed in charge of the CIA),
D. Bleeding Stupid, or
E. Some combination of the above traits.
All the Central Intelligence Agency need to release documents belonging to the U.S. army, or any other arm of the U.S. executive branch is either permission from the executive department itself (it's happened) or just a willingness to go over said the departments' head (it's also happened, albeit less often, because that gets people fired).
The Central Intelligence Agency, during the course of the Cold War, manipulated rebel groups and political processes in many nations (particularly in South America) to create dictatorial regimes in order to prevent the creation of any government that might support the Soviets, and worked to undermine the Soviet government in the USSR and elsewhere as much as they could. Quite a bit of what they did was blatantly illegal by the standards of U.S. law, and as such was kept hidden from the general public until the last few decades.
The CIA is depicted as being at odds with itself and other government institutions for precisely the reason listed above; whenever anyone inside the CIA or outside of it learns of and decides they dislike the CIA's policies, conflict happens. This is part of the reason why the modern CIA is actually very understaffed, because its members tend to quit and go work for private military contractors or other, more honest institutions.
Theoretically, the CIA is ultimately directed by the President himself, but there have been administrations in the CIA that blatantly and directly lied to the President and Congress in order to get more funding and cover up their mistakes. There have been other times in which the executive branch basically controlled the CIA directly (particularly during the Nixon administration).
The modern Central Intelligence Agency is not the super-spy organization that many people think it is. Even at it's height, the CIA only had a few super-spies, and today it's better known for delivering misinformation or inadequate information and being generally ineffective. It lacks the direction, the manpower, and especially the popular support needed to reform itself. It's kind of sad, really, when you consider what it could have been...
Interesting that the media helps make these zealot stupid conspiring crooks into pop heroes in multimillion dollar movies. Jason Bourne and 007 my a**.