I agree with those who think you are trying to cover a lot of ground in 10 days.
The SBB website shows that Zurich airport to Mürren is more like 3.5-4 hours than "8 to 9 hours;" it does include multiple train changes. Mürren to Rothenburg ob der Tauber is indeed 9 to 11 hours with numerous changes; it seems to me like that is an enormous loss of time for your short trip. I honestly wouldn't want that kind of travel day as an adult on a 3-week trip; I can't imagine doing it with an 8- and 10-year-old on a 10-day trip.
I agree with Tim that your time in Mürren is a little short, and Jungfrau is worth seeing (if sunny). I also like Jill's idea of thinking more regionally. I think Mürren-Luzern would be a great trip that is not so rushed. Luzern has an excellent transportation museum, a nice lake promenade, and Mt. Pilatus. Mt. Pilatus has a ropes area for kids, a Sommerrodelbahn (toboggan run), a playground, and other activities. Munich-Salzburg is also a nice trip perhaps with a day trip from Munich to Garmish-Partenkirchen for the Zugspitze (the tallest mountain in Germany) and/or Partnachklamm (a gorgeous gorge) and a day trip from Salzburg to Berchtesgaden for Königssee, a beautiful lake surrounded by mountains -- touristy at the main entrance but excellent, non-touristy, family-friendly hiking at the far end of the lake. See here, here, and here for thoughts on Salzburg for kids. If you really want mountains, though, Switzerland is the place to be.
If you are committed to Mürren and Munich as book ends to the trip, you could just have a long travel day to Munich and skip the middle stop (7.5-8.5 hour travel day). If you want to make a stop, I would think about somewhere that is along the train lines that run between the two locales. One way to make the journey from Mürren to Munich is through Basel to Karlsruhe and then onto Munich. For a small-town, split-timbered building experience (something like Rothenburg without so many tourists), I would think about Gengenbach, which is a short train ride from Offenburg (which is on the Karlsruhe to Basel train line). If you spent two nights there, you could use your full day to explore a town deeper in the Black Forest or to go to the outdoor Black Forest museum that chronicles life in the Black Forest with old houses, animals, and live demonstrations; there is a Rodelbahn near the outdoor museum. The other Mürren to Munich option takes you to Zurich and passes Bodensee/Lake Constance. There are several cities/towns from which to choose. Lindau is on the train line and would give the shortest train ride (a little over 5 hours). It's a cute little town with a nice waterfront. For your day on Bodensee, you could consider the flower island Insel Mainau (a little bit of a long trip to get there), the medieval castle at Meersburg, the zeppelin museum at Friedrichshafen (zeppelin rides available, though I have no idea what the cost is), or a number of other activities.
The travel direction Mürren to Munich has the advantage of not needing to move the final night of your trip to be close to the airport for your flight out of Europe. The travel direction Munich to Mürren has the advantage of minimal travel on Day 1 plus one other advantage... ending the trip at the grandest place.