It would be part of the unwritten history of the Corleones, and as someone points out there is a foreshadowing of this in GF Returns the horrid novel.

However, I agree with the idea that there is enought in the GF movies to suggest that they would have been part of the mob operation which supposedly played a role in the JFK assassination. As one conspiracy theory goes, rogue elements in the CIA teamed up with the mob to do the hit. The mob tie had something to do with the fact that JFK made a deal never to invade Cuba after the missile crisis, which meant that the mob lost its investments in Havana to the Commies. The mob also thought it had helped JFK, whose father had connections win a crucial primary in West Virginia, as well as the state of Illinois by helping fix the vote in Chicago. Then, the theory goes, JFK went squishy on Cuba, and RFK started to go after the mob, so in essence they felt betrayed.

In GF II Hyman Roth says that with the deal done in Cuba, they finally had an entire country under their thumb, and then he goes on to say with the right man and enough money they could get someone elected to be the president of the United States. There is little doubt in my mind who FFC was referring to when this scene was shot many years after the JFK assassination, and after these conspiracy theories began making the rounds.