I'm not knocking Harbaugh's coaching career. He did have trouble getting his feet back on the ground coming back to the college game, not the least because he had not been able to recruit a top level QB to lead his teams - some of which probably had enough talent to get to and maybe win the playoff if their offense had had an NFL draft quality QB. But he has now brought the program back to a level as high as it has ever been. But now he has to decide whether the joy is in the chase or in the keeping, and since his success at most of his stops has been closely tied to his QB it would be hard to believe an opportunity like the possibility of coaching Williams at Chicago wasn't something that would at least pique Harbaugh's interest.
He's clearly a person whose motivations have an internal logic which is not evident to the external observer, so who knows what is really most important to him. At different times it has appeared to be his school, a superbowl win, more money. Maybe all three at once depending on the day of the week.