The biggest bone of contention between Harbaugh and the Niners is control: Harbaugh wants final say over the 53-man roster and GM Trent Baalke isn't going to give it to him. I'm sure Michigan would be more than happy to give him final say over the roster, as would a number of NFL teams. The report is that Harbaugh would prefer to stay in the NFL, and there will certainly be a number of teams looking to work a deal with San Francisco (Harbaugh still has a year left on his contract) to get him.
I don't think there's any question that Harbaugh will be a head coach somewhere next season--like him or not, the guy is good at what he does. But it certainly won't be in San Francisco; the relationship there between coach and front office has become too dysfunctional for it to ever work.