No, John F. Kennedy was not assassinated due to his opposition of Israel's power, but due to the work of a lone, mentally ill gunman, Lee Harvey Oswald. Oswald suffer from many psychological disorders that had not been properly diagnosed and treated, and the President lost his life as a result.
"Israel will endure and flourish. It is the child of hope and the home of the brave. It can neither be broken by adversity nor demoralized by success. It carries the shield of democracy and it honors the sword of freedom" - John F. Kennedy.
Kennedy fought the Israeli lobby within the United States, which is not the same thing at all as being against the State of Israel. While I'm sure extremists exist in pockets of the world who would be happy to assassinate him for that, the Israeli lobby did well enough playing the game that they had little motive to break the rules.
Besides, Lee Harvey Oswald had Soviet sympathies long before assassinating Kennedy. Russia has a history of being anti-Semitic, so if anything, I would expect Oswald to be apathetic to or somehow against Israel in general.