And speaking of movies (since the OP is about movies), Enter Nowhere was a pretty good time travel film and one of the four characters was a Nazi soldier from the middle of WWII who was not portrayed as evil. Plus the play Copenhagen treated Heisenberg very sympathetically, and he was the head of Germany's nuclear program during the war; Benedict Cumberbatch voiced Heisenberg in a radio adaptation.

I'm not a huge film buff, so I'm sure there are others.