I think FDR would defeat Dewey fairly easily. Remember that whatever their reservations about Willkie, most anti-interventionist leaders (including John L. Lewis) did vote for him. The Willkie forces even took out advertising space in the
Daily Worker (the Communists of course then being opposed to the "imperialist war")!
https://books.google.com/books?id=iWMprgS8q0AC&pg=PA269 So I doubt that Dewey could get a larger anti-war vote than Willkie, whereas some Republican and independent internationalists who supported Willkie might well refuse to vote for Dewey.
In any event, it was not so much Dewey's isolationism (or "anti-interventionism") that made him lose his front-runner status after the fall of France--after all, Taft and Vandenberg still had considerable support. Rather, it was the feeling that someone as young and inexperienced as Dewey could not be trusted to deal with the dangerous world situation. As someone joked, Dewey had become the first American casualty of World War II...