At the time of the Cuban missile crisis, the Communists had been entrenched in the Soviet Union for over 40 years. Domestic opposition, including post-World War II guerrilla warfare in the Baltic States and Ukraine, had been ruthlessly crushed well before 1962. Millions of regime opponents were killed in the Gulag under Lenin and Stalin. Those Russians and others who had fled Communism were in no position to take power over such a vast nation from their exile in places like Paris or New York. The Soviet Union was far more powerful than Cuba, and Communist rule was not dependent upon the charisma of one man. Assassinating Khrushchev would have only resulted in another Communist taking power, just as the assassination of Kennedy (or for that matter Lincoln, McKinley, or Garfield) did not cause our government to collapse.
Assassination is a tool that would have worked against the Cuban regime, but not against the Soviet dictatorship. I doubt anyone in a position of responsibility in the 1960s considered assassinating Khrushchev.