But by all indications, the 49ers now see him as expendable.
That's been the message for the past 10 months, since the club entertained the idea of trading him to Cleveland, and that drumbeat has gotten louder in recent weeks, especially since San Francisco's spirit-crushing, 19-3 loss to Seattle on Thanksgiving night.
Those four words have echoed throughout the franchise for the past eight days, and were followed by a forehead-slapping outburst from the college-age daughter of 49ers General Manager Trent Baalke, who used her Twitter account to give the team's offensive coordinator — and Harbaugh protege — his unofficial walking papers.
"Greg Roman can take a hike," Cassie Baalke wrote on her since-deleted account. "The 49ers don't want you no more."
Ah, kids say the darnedest things. There's no denying San Francisco's offense has been a bust lately, failing to score more than 17 points in five of the past six games. Once the most dynamic weapon in the game, quarterback Colin Kaepernick hasn't been as consistently dangerous as a passer or runner this season.
Kaepernick's relationship with the San Francisco-area media seems to get testier by the week. He was asked 17 questions during his mandatory session with beat writers this week, and he responded with a total of 88 words, that's 5.2 words per answer for those keeping score at home.
Then again, what is there to say? Harbaugh too has been in no mood to give any deep, introspective answers about his future with the franchise, especially after reports surfaced over the weekend that the 49ers were mulling a trade with Oakland or the New York Jets. There's a snag to that: He reportedly would have to OK such a trade, which would be surprising because it would mean going to a bad team that presumably would have to give up draft picks to get him.
Harbaugh is under contract through next season, and it could be that he forces the team to fire him and pay him for the final year of his deal.
The intrigue grew this week when Harbaugh's alma mater, Michigan, fired coach Brady Hoke, possibly clearing the way for the 49ers coach.
On Monday, Harbaugh told reporters that his offensive coordinator has his "unwavering support," and that he did not speak with York over the weekend.
"I don't worry about my future," Harbaugh said. "I haven't participated in any of that speculation. I think I have a recessive gene for worrying about my own future."
According to multiple reports, and insiders knowledgeable on the inner workings of the 49ers, there's a wide chasm separating Harbaugh and the tandem of York and Baalke, and not much healthy communication is going on between the sides.
Harbaugh is famously moody and combustible. He also made an instant impact on the three programs he has coached — the University of San Diego, Stanford and the 49ers — turning them into winners, even though his personality rubbed some people the wrong way. Last year, John Madden said Harbaugh's 2011 season was unrivaled.
"We tend to put everyone in the Hall of Fame when they have a great game, or say everyone's great when they do one good thing," Madden said during an interview at his San Francisco condominium. "I kind of think that Jim Harbaugh's first year, by getting to the championship game, was the best coaching job in the history of the NFL.
"Just in my mind, the time that I've studied the game, someone that had all those things stacked against him. There was a lockout, so he didn't get to work with any of the players. He couldn't put his program in. He had to take what was there, he had no time for free agency. And he made the best of it and got to the championship game, came that close."
There are many people who believe that Harbaugh is gone after this season, even if he were to win a Super Bowl. To make the playoffs, the team probably will need to run the table against its final four opponents: at Oakland, at Seattle, San Diego and Arizona.
By every indication, the 49ers believe that Harbaugh is an interchangeable cog in the machine, and they can keep winning with the structure they have in place, and with Baalke picking the players. That might be the case, but it's a risk. San Francisco, which fired Steve Mariucci after the 2002 season, cycled through Dennis Erickson, Mike Nolan and Mike Singletary before finding a coach who made the franchise relevant again.
For now, the Harbaugh family slogan that became a team mantra has become something of a punch line.
"Who's got it better than us?"