Here's the historian Robert Dallek on the plots and how much JFK knew about them. Dallek is a mainstream liberal historian and his book on JFK is, let's say, not exactly hard hitting.
From "An Unfinished Life: John F. Kennedy 1917-1963":
"No secrets on foreign policy existed between them [RFK and JFK]. Assassination was undoubtedly a topic of discussion and something the emotional, messianic Bobby may have seen as a necessary evil. But his more dispassionate brother seems to have resisted the suggestion, not necessarily as immoral, but as impractical and counterproductive. Kennedy realized that Castro’s death seemed likely to strengthen rather than eliminate communist control in Cuba, where the leader’s brother Raul and Che Guevara could convert his death into an emotional plea vindicating his life and beliefs. Poor planning at the Bay of Pigs had ended in disaster. By contrast, careful, modulated responses to Khrushchev’s pressure over Germany and Berlin had produced at least a temporary stand-down. The two episodes had strengthened Kennedy’s instinctual caution about any response to international dangers that could lead to war. Although the CIA continued to see assassination as a possible response to pressure to remove Castro, there is no evidence that the White House, perhaps after briefly entertaining it, saw it as anything more than a bad idea."
I think that's deeply misleading - "perhaps briefly entertaining it" and "no evidence" for it? Perhaps? No evidence at all?
