Still, uncertainty lingers in San Francisco. The relationship between Harbaugh and Baalke has been portrayed as the major source of internal dysfunction, but that might not be the only area of concern.
Ann Killion of the San Francisco Chronicle reported Sunday that "Harbaugh's act has worn thin in the locker room, particularly among some key 'face of the 49ers' type players," according to a source with inside knowledge of the team.
This probably doesn't come as a surprise -- Harbaugh never will be confused with Pete Carroll, after all. As for the "face of the 49ers" bit, names like Frank Gore, Patrick Willis, Justin Smith, Vernon Davis and Colin Kaepernick immediately spring to mind.
Another 49ers source believes that even a rich, new contract would provide only temporary tranquility within the organization.
"That's just who Jim is," the source said. "He'd probably like to redo his contract every year, just out of competition."
These are the type of quotes that make it sound like Harbaugh's more trouble than he's worth. But then you remember the Niners have averaged 12 wins for the past three seasons with three deep playoff runs, including one near Super Bowl triumph.
As long as that success continues, Harbaugh will continue to possess supreme leverage.
The latest edition of the "Around The League Podcast" works through our top 101 free agents and responds to some heat from Donte Whitner.