I don't agree. I think the remark WAS refering to Kennedy and it was simply an anachronism. The last president assassinated before Kennedy was McKinley and that was some 60 years before Michael would have said that line.

Further to this, in the second draft of the script (pg 95) there's mention of the skimming process that the Corleone Family followed and it refers to a family courier having a flight layover at Kennedy Airport (before continuing on to Geneva with the skimmed money). The New York airport was then named Idlewild (before Kennedy was killed). Its one of the sloppy details that were apparent in Part II (despite it being an extraordinary movie).