Going against the CIA can be bad for your health. JFK found that out.
While I am sure many CIA guys were not unhappy to see JFK whacked its involvement came with the cover-up. “The Ultimate Sacrifice” lays out what I believed happened. The mob had infiltrated a top secret operation to be launched against Castro and was able to, through one of their operatives-Lee Harvey Oswald, force a cover-up for fear of starting a nuclear war.
Many of the figures in that plot had connections both to the Agency and to the Mafia. Both Carlos Marcello and Santos Traficante admitted prior to their deaths to their lawyers that they were responsible for the assassination.