The CIA did assassinate JFK.
There are clear motives: the failed Bay of Pigs operation and terminated plans to kill Fidel Castro. JFK was first mad at the CIA because of the Bay of Pigs and he never forgave the agency for the public embarrassment. He threatened to smash the CIA into a thousand pieces and scatter it into the wind. On top of this, there are contracts between the CIA and organized crime to assassinate Castro. JFK immediately terminated these plans and sent the FBI and law enforcement to break up the CIA training camps. There is no doubt that the two had growing conflict. After the assassination, the Warren Commission sat for ten months and never hired any investigators and relied on the FBI and CIA to investigate. To no surprise, they found themselves innocent. The agency never even disclosed information about the previous plans to kill Castro to the Commission. Let's not forget a possible connection between the CIA and Lee Harvey Oswald. Around September-October of 1963, Oswald went to Mexico City and attempted to get visas from the Soviet and Cuban embassies but he failed. The agency denied knowing about this trip but documents show that they did have pre-assassination knowledge. The CIA cannot be trusted. Based on their quick response, cover-ups, and withholding of important information from the Warren Commission, the CIA obviously has something to hide.