During his presidency, John F. Kennedy had numerous disagreements with the CIA. Their conflicting opinions for military operations could have led to the government assassinating the president. Kennedy and the CIA both blamed each other for the disastrous results of the Bay of Pigs invasion that occurred in 1961. Supposedly, after the operation JFK made personal changes that upset other CIA members. The growing resentment could have led to a plot to assassinate Kennedy. In addition, JFK disagreed with the CIA's plan to assassinate Fidel Castro and didn't want to allow the operation. This is another possible motive for the CIA to kill Kennedy. The former head of the CIA, Allen Dulles, was on the Warren Commission so had influence over what was included in the report.
Just because President Kennedy and the CIA had disagreeing opinions on military operations does not mean that the government would assassinate the president. Planning and performing that complex of an operation would have been near impossible to keep secret from Kennedy. The aftermath of the assassination was messy and was not beneficial enough to to the CIA to have been planned by them.
[P1] JFK and the CIA had many disagreements. [P2] The head of the CIA was on the Warren Commission. [P3] Therefore, the CIA had a motive to assassinate JFK.
Rejecting the premises
[Rejecting P3] These things are not enough to form a believable motive.