You can certainly make a connection between Roth returning to America "to vote in the Presidential election" (1960 election), his assassination and JFK's assassination. Probably FFC intended us to make that connection.
But I find Michael's statement, "If history has taught us anything it's that you can kill anyone" more connected to what he told Kay in GF when he wooed her in New Hampshire. Michael had said that his father was "no different than any other man with responsibilities toward others." Kay replied that "Senators and Governors don't have people killed." Michael said, "Now who's being naive...." Right there, we had Michael's rationale for "legitimization"--he and his father were behaving no differently than the pezzanovanti in politics. And that's exactly what he did when he ordered Roth's murder.