I, too, am a fan of Rothenburg. People have mentioned some alternatives here, Landsberg, Mittenwald, but they aren't the same as Rothenburg. There are things that you can do that don't get you involved in the tourism culture. We spent half a day walking the Wehrgang on the wall and seeing the museum in one of the towers. There were hardly any "tourist" there. Also few at St. Jocobs church, with it's Riemenschneider Alter. We avoided Kathe Wohlfahrt's Christmas shop and the Crime and Punishment Museum - too touisty.
It would be a shame to visit Germany and not see Rothenburg, but it would be a trek from Munich for a day trip, but not impossible. If you used a 31 euro (for two) Bayern-Ticket and regional trains you couldn't get to Rothenburg before almost 1 PM, but with an advance purchase ticket using an ICE through Nürnberg you could easily arrive before noon. Combined with a Bayern-Ticket-Nacht and getting back to Munich late, you could make the trip for about 76 euro and spend about 7 hours in Rothenburg.
Nördlingen is another medieval, walled city, about half the travel time from Munich, and, like Rothenburg, has a wall with a walkable Wehrgang. It's kind of a less touristy version of Rothenburg, without a Christmas shop or Punishment Museum.