After Sunday's debacle in St. Louis, Harbaugh might want to do it again.
That Colin Kaepernick is a fine young talent who may someday win a Super Bowl for the 49ers or some other team isn't up for debate. He has a rare combination of size, running ability and arm strength to win a lot of games for a lot of years in the NFL.
It's why Harbaugh was so star struck after Kaepernick's first start against the Bears on Monday night two weeks ago that he kept him on the job. It's why Smith watched from the sidelines once again against the Rams despite a clear head and some sterling credentials of his own.
Four games away from the playoffs, though, the steady hand of Smith might be the best ticket the 49ers can punch to get to the Super Bowl in New Orleans.
Except Harbaugh seems as smitten with his second-year quarterback as ever.
"It was a tough game for a quarterback to play in," Harbaugh said. "I thought he did well."
At times Kaepernick certainly did, particularly when he made up for a series of miscues with a spectacular 50-yard scramble that put the 49ers in position to win the game against the Rams. But the drive ended with a field goal, the game went to overtime, and the Rams finally ended it with a late kick for a 16-13 win.
Had the Rams not put those points on the board with 26 seconds left in OT something other than a quarterback controversy might be the legacy of the game. It could easily have been the second tie game between the two teams in three weeks—something that was such a long shot even Vegas oddsmakers wouldn't put a price on it.
Instead, the focus for 49er fans will be on a quarterback controversy that didn't need to be.
Argue all you want about Kaepernick's potential and ability—he certainly has plenty of both. But don't forget Smith took the 49ers to within a field goal of the Super Bowl last year and his only mistake this year was to suffer a concussion that forced him off the field in the tie against the Rams in San Francisco.
"I feel like the only thing I did to lose my job was get a concussion," a somewhat perplexed Smith said earlier in the week.
Not that anyone should feel sorry for Smith. The former No. 1 pick had his chances but didn't play well in a variety of different schemes in San Francisco before finally flourishing under Harbaugh in a breakout season last year.
That won him a new $33 million contract, with $16.5 million guaranteed. But it didn't stop the 49ers from almost straying a few months later when they took a close look at free agent Peyton Manning before deciding to stick with the quarterback they had.
And it didn't stop the coach/quarterback guru from sticking with Kaepernick even when Smith was cleared to play, declaring he would go with the quarterback with the "hot hand."
That hand wasn't so hot Sunday in St. Louis against a defense that seemed to confuse Kaepernick at times. His numbers were decent enough—208 yards passing and another 84 rushing—but he got the 49ers into the end zone only once and made two critical second-half mistakes that allowed the Rams back in the game.
The first gave St. Louis its first points when Kaepernick was called for grounding while trying to scramble from the end zone. The second hurt far worse, when Kaepernick pitched the ball over Ted Ginn Jr. deep in 49ers territory and the Rams recovered for a tying touchdown.
"I was just trying to make a play instead of playing it safe," Kaepernick said. "I should have kept it and let the clock run. Let your punter get on the field and let our defense play."
Mistakes of a young quarterback, part of the growing process in the NFL. Kaepernick will make more of them, but his upside is so tantalizing to Harbaugh that he's willing to risk a loss here or there to have him under center.
But is he willing to risk a Super Bowl run for a team already primed for one behind Smith? Will he keep a quarterback on the sidelines who was fifth in the NFL with a passer rating of 104.1 and had a 70 percent completion percentage when he suffered the concussion that benched him?
Is he so confident in his ability to analyze the quarterback position that he will stubbornly push ahead with Kaepernick no matter what?
"I'll let you know if there's a change but right now I think it'll be the same as it was this week," Harbaugh said. "I'm proud of Kap, proud of the way he played. He did some really good things under a lot of heat and duress and handled himself well, gave our team a chance to win."
Tough to second guess Harbaugh, who took over a hapless 49er team last year and nearly made the Super Bowl with them. He understands talent and he knows the quarterback position better than anyone in the NFL after spending 14 seasons taking snaps on Sundays himself.
But you can't help wondering if he's taking a chance he doesn't need to take.
Tim Dahlberg is a national sports columnist for The Associated Press. Write to him at tdahlberg(at)ap.org or http://twitter.com/timdahlberg