You can reduce the ground travel distances by substituting for Freiburg and Heidelberg cities that are closer in but similar in character. Consider Regensburg (UNESCO World Heritage old town,) Landshut, Nuremberg, Augsburg, Ulm, or possibly some smaller places... Landsberg am Lech, Harburg, and Nördlingen for example, on the Romantic Road north of Füssen. All these places are in Bavaria. Here's a map. I think your original plan will mean more than 1,000 km of driving.
H'berg and Freiburg are nice but IMHO are somewhat less interesting than most of the options above anyway (and that would be true even if they were closer to Munich.)
Consider also the extensive rail network in Bavaria for getting to these places. I don't see a car as an convenience or as a savings advantage for most of these destinations.
Detailed rail line map:
https://www.bahn.de/regional/view/mdb/pv/deutschland_erleben/bayern/regionales/diverses/2015/mdb_185091_20130717_sk_by.pdf