Maybe come back up from Munich via Ulm and Stuttgart on the way back up to Frankfurt? What do you enjoy seeing?

Stuttgart has frequent train service between both Munich and Frankfurt. Any decent sized town will have a Christmas market in the town square to visit.

Another option would be to go to Prague for those two days. There is a direct train from Munich but I'm not sure about getting to Frankfurt by direct train, although you'd probably just have to connect in Dresden or Nürnberg.