The bigger long-term concern is a potential rift with the front office.
There have been many reports spelling out the differences between general manager Trent Baalke and Harbaugh. While 49ers CEO Jed York vocally dismissed a report that the team worked out a trade with the Cleveland Browns for Harbaugh, the organization has remained mostly quiet regarding all the reports of in-house friction. NFL Media columnist Michael Silver reported that the 49ers "weren't inclined to beg" to keep Harbaugh around.
It raises this possibility, which NFL Media's Albert Breer brought up Monday: Could Harbaugh turn into this generation's Bill Parcells?
The Parcells model was well established by the end of his career. Pick an also-ran team, build up the organization from the field to the front office with "Parcells guys," create some drama and get out of town.
Harbaugh hasn't stayed in one place for long as a head coach. As a source told the Chronicle's Ann Killion, the organization seems to "thrive on chaos and distraction."
The 49ers want to avoid the uncertainty because it could be a distraction throughout the 2014 season. (Think of the reports of Parcells negotiating with the New York Jets in the same week he was coaching the New England Patriots in the Super Bowl.)
This scenario would be a growing possibility if Harbaugh and the 49ers don't progress on a potential long-term contract this offseason. Harbaugh wants to be paid like a Super Bowl winner, and the organization doesn't want to go that far. There is trepidation about handing the keys of the team over to Harbaugh for good.
Without a new deal, the reports about interest in Harbaugh are only going to pick up in the winter. We'll inevitably start to hear weekly rumors that big name colleges (Michigan?) or troubled NFL franchises are interested in Harbaugh. These reports bubbled up during and after the 2013 campaign, but they would grow exponentially if Harbaugh's contract remains unresolved.
Harbaugh has a dominant personality that might work better in short spurts. His abrasive and aggressive management style, like Parcells', is effective at making systemic changes. But can that style grow old? Even at Stanford, there was a sense it was time for Harbaugh to move on to another challenge in order to leave the program in the capable hands of David Shaw.
Both sides could be receptive to Harbaugh's departure after the 2014 season. The 49ers see Baalke as a potential lifer in the organization. Harbaugh already feels like a year-to-year proposition.
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