I don't think there's a good way to execute that kind of story.
Ummm, there have been a whole bunch of stories over the years where high fantasy and/or the supernatural elements have been effectively integrated into the WWII setting, and there's no reason whatsoever that the trappings of Rowling world of wizardry couldn't work just as well within that framework than, let's say, the supernatural aspects that were the focus of the first and third Indiana Jones films.
The notion of Dumbledore as a high ranking member of a secret branch of military intelligence, using magic to fight the Nazis sounds pretty darn entertaining to me.