Kennedy authorized the coup, the only thing he was naive about was he believed that Diem and his brother Nhu would be allowed to leave the country in exile. The one who really had it out for Diem was Averell Harriman who spent months coaxing Kennedy into plotting his overthrow.
"(President Kennedy): I was shocked by the death of Diem and Nhu. I'd met Diem with Justice Douglas many years ago. He was an extraordinary character. While he became increasingly difficult in the last months, nevertheless over a ten-year period he'd held his country together, maintained its independence under very adverse conditions. The way he was killed made it particularly abhorrent."
JFK'S MEMOIR DICTATION ON THE ASSASSINATION OF DIEM
The other information that has been brought up since Nov. 22, 1963, is that at the time of his death, JFK , was planning on eventually withdrawing all U.S. troops from Vietnam. From a 2003 article by James Kenneth Galbraith, which he bases on the meticulous work of John M. Newman. "Newman was a Major in the U.S. Army, an intelligence officer last stationed at Fort Meade, headquarters of the National Security Agency. As an historian, his specialty is deciphering declassified records—a talent he later applied to the CIA’s long-hidden archives on Lee Harvey Oswald."
Exit Strategy: In 1963, JFK ordered a complete withdrawal from Vietnam
The article states that from October 2nd, 1963, Kennedy was planning on withdrawing U.S. troops, after receiving a mission report completed by Robert McNamara and Gen. Maxwell Taylor. The article also states at that same meeting: "At Kennedy’s instruction, Press Secretary Pierre Salinger made a public announcement that evening of McNamara’s recommended timetable for withdrawal."
Newman made a chronological summery of the decision to withdraw troops, based on documents, info, etc. His second point is interesting, because:
"On October 5, Kennedy made his formal decision. Newman quotes the minutes of the meeting that day:
'The President also said that our decision to remove 1,000 U.S. advisors by December of this year should not be raised formally with Diem. Instead the action should be carried out routinely as part of our general posture of withdrawing people when they are no longer needed.'"
So this decision was focusing on December, and Kennedy was under the impression in early October, that Diem would still be in power in December, but that they wouldn't discuss the withdrawal with him before-hand.
So why assassinate the President of a country, you are planning on withdrawing your troops from? I do not believe that John Kennedy authorized the assassination of Diem, his younger brother, or the secret police chief, all at the same time. and in the way it was conducted.