This "wearing out the welcome" thing is not imagined - even Harbaugh himself frequently acknowledges that it exists - he is sometimes so 'over they top' competitive & sometimes to the point of offending people.
Towards the end - it was not all sweetness & light at Stanford - oh it did
not get super ugly - but you can figure that the folks at Stanford are quite happy with the coach they have now
Just one article for example -
http://espn.go.com/blog/bigten/post/_/id/113365/harbaugh-will-win-big-but-for-how-long
"There are also many stories of Harbaugh clashing with Stanford administrators over admissions policies and other issues. Our sympathies in advance to any Michigan higher-ups who try to tell their new coach no on something."
Harbaugh is good - very very good - but often his restlessness / relentless competitiveness ends up seeing him moving on - before he has reached his ultimate goal ... now maybe a College National Championship was too much to expect at Stanford - but he certainly got them in to some of the conversations ... maybe a Super Bowl ring was still possible with the 49ers - he got oh so close ... but it appears that Harbaugh is built for a powerful beginning leadiing to the apex of his performance - and then on to a new challenge .... not sure he is wired to stay in one place and go through natural cycles of build - rise to top - rebuild - rise again - rebuild again ....