There are aspects of foreign policy that have been, since 11/22/63, and will seemingly always remain, in the hands of the Military-Intelligence complex. The last president who stood up to the MilInt complex was John Fitzgerald Kennedy, who after the Bay of Pigs fiasco famously stated that he wanted to "break the CIA into a thousand pieces."
JFK defused the Cuban Missile Crisis largely by standing up to the military brass, who wanted full scale war up to and including a nuclear exchange, and went on to open back channel diplomacy with Premier Krushchev of the USSR and even Cuba's Fidel Castro. On several occasions shortly before his death JFK told close associates (who have been quoted in numerous books - too numerous to mention here) that following his re-election in 1964 he intended to remove all US military advisers from South Vietnam.
His famous American University speech of June 10, 1963, titled "A Strategy For Peace" (see http://en.wikipedia.org/wiki/American_University_speech) was almost certainly the final nail in his coffin. Kennedy proposed, in effect, his intention to radically de-escalate, if not end, the Cold War. There was no way on earth that the MilInt complex could allow JFK to live given the policies outlined in that speech and his intention to disengage from Vietnam. Far too much money and power was on the line for JFK to be allowed to go on, President of the United States or not.
To this day I suspect two things, the first being that the Vietnam War was extracted from Lyndon Johnson as the price for allowing LBJ to pursue his Great Society dreams, and secondly, that it has been "explained" to every Democrat elected to the presidency since that there are sharply circumscribed limits on his power to affect certain aspects of the foreign policy that the MilInt complex and other Powers That Be wish to pursue. And the example of what became of John Kennedy is used, whether obliquely or explicitly, to explain the price of defying those power centers. Unsurprisingly, Democratic presidents have caved in rather than be rubbed out as Kennedy was. Republicans don't need to be threatened. They've been in bed with these powers since the days of Nixon.
There are simply things even Presidents are not permitted by TPTB to do. Read James Douglass' "JFK and the Unspeakable" and your questions about the whys and wherefores will be answered.