San Francisco 49ers quarterback Alex Smith (11) and quarterback Colin Kaepernick (7) warm up before an NFL football game at the Louisiana Superdome in New
San Francisco 49ers quarterback Alex Smith (11) and quarterback Colin Kaepernick (7) warm up before an NFL football game at the Louisiana Superdome in New Orleans, Sunday, Nov. 25, 2012. (AP Photo/Gerald Herbert)

SANTA CLARA -- Jim Harbaugh is doing what he must do. He shouldn't apologize, and he is not apologizing. The 49ers coach is paid to win football games. The NFL is the country's largest sports business entity. It is brutal commerce with cheerleaders and slow-motion replay.

Wednesday, that commerce included the official naming of Colin Kaepernick as the 49ers' starting quarterback for Sunday's game in St. Louis and probably beyond. Kaepernick replaces previous starter Alex Smith, who on Nov. 11 left the first half of a game at Candlestick Park when he said his vision was blurry. He was diagnosed with a concussion.

San Francisco 49ers quarterback Alex Smith (11), on left, throws the ball as quarterback Colin Kaepernick (7) watches during practice at the San Francisco
San Francisco 49ers quarterback Alex Smith (11), on left, throws the ball as quarterback Colin Kaepernick (7) watches during practice at the San Francisco 49ers Fan Fest at Candlestick Park, San Francisco, Calif., on Sunday, Aug. 12, 2012. (Josie Lepe/Staff)

Since that moment, Smith has not taken a competitive snap, even though he was cleared by doctors to play last Sunday in New Orleans. Kaepernick has started the last two weeks for the 49ers and won both times, showing some moxie and skill. Harbaugh, however, has mostly danced around the issue of whether this makes Kaepernick or Smith the "real" starter moving ahead.

"Both have earned it," Harbaugh said again of the job Wednesday before announcing: "Colin has the hot hand. We'll go with Colin."

In truth, it is more than "a hot hand." If anything, Harbaugh was bending over backward in being diplomatic to Smith. Anyone with a half-educated football eye can see that Kaepernick is bigger and faster than Smith, with a stronger throwing arm. The 49ers can win with either quarterback, but Kaepernick might make three or four plays a week that Smith can't. Giving Kaepernick the nod is clearly the right call for this week in pure football terms and in commerce terms.

But the choice Harbaugh made is still dangerous and fraught with risk. For a couple of reasons. One is less perilous than the other.

Any time a coach decides to bench a veteran player who is popular in the locker room -- and Smith was elected the 49ers' offensive captain by his teammates -- there is the chance that roster chemistry will be discombobulated.

San Francisco 49ers quarterback Alex Smith (11) gives a high-five to colleague Colin Kaepernick (7) after completing a touchdown pass against the San Diego
San Francisco 49ers quarterback Alex Smith (11) gives a high-five to colleague Colin Kaepernick (7) after completing a touchdown pass against the San Diego Chargers in the first half of a preseason game at Candlestick Park, in San Francisco, Calif., on Thursday, Aug. 30, 2012. (Ray Chavez/Staff) (Ray Chavez/Staff)

Smith likely won't be fomenting that discombobulation. He is a professional who has been through worse than this. In the NFL, lots of unfair things happen. Smith understands that being disgruntled will get him nowhere, either this season or with a future employer. But if 49ers veterans believe that Smith has been treated shabbily, it could create attitudinal issues -- especially if they start fretting about whether they might lose their own starting jobs through injury, an unwritten no-no in pro sports.

The initial player reaction to Kaepernick's promotion was as you would expect: Praise for both him and Smith, focus on the task at hand.



"Alex is a great player, a great person," said offensive lineman Alex Boone when asked how he thought Smith (who was not available for comment) would react to the move. "He's a team-team-team guy."

"I'm not surprised by anything," said wide receiver Michael Crabtree when asked about the quarterback decision. "I don't worry about that. I just worry about my job. I'm trying to play my position."

In the end, that part will take care of itself. Kaepernick will play and the 49ers will either win or lose. The team mindset is all internal stuff that Harbaugh is -- let's say it again -- paid to handle. His record shows he will and he can. It's not your usual path to the Super Bowl when you make a late-season quarterback switch from one of the league's top passers (as Smith is, according to statistics) to a relatively untested second-year man. But Harbaugh has been unconventionally successful all along.

The other and more serious danger of Harbaugh's decision is far more troublesome because it involves future player safety. Given the way Smith's concussion story line played out, shouldn't there be a concern that other 49ers will be reluctant to self-report their own woozy heads?

"That would be something to worry about," Harbaugh acknowledged. "I would never want that message to be sent to our players."

The problem is, the message already has been sent, intentionally or unintentionally.

The blow that led to Smith's concussion Nov. 11 occurred early in a drive that led to a touchdown. He stayed in the game, called and executed plays while completing three more throws, including the scoring pass to Crabtree. Only then did Smith come off the field and tell trainers he felt strange. If he had not said so and had gutted out the rest of the afternoon, would he still be the starter?

The implication is yes, if you believe Harbaugh's contention that Smith is still a starting quarterback. Why would he have come out of the game that day if he had not reported any symptoms? The 49ers are very involved in NFL concussion protocol, with team owner Dr. John York serving as chairman of the NFL Committee on Health and Safety. The fallout of Smith's situation should prompt some interesting discussion.

"I think if you truly had a concussion," said Boone, the offensive lineman, "you are going to report it."

"I think you have to be smart enough about it and worry about your own health," fullback Bruce Miller said.

Harbaugh's feelings about all of this are pretty transparent, even if he tries to hide them. He thinks people are making too big a deal about the quarterback folderol. And he's right. The 49ers are still a defensive-based team and offensively will continue to rise and fall mostly on the shoulders of running back Frank Gore.

Yet forever and always in the NFL, quarterback decisions do matter. If the 49ers don't win it all this season, Harbaugh will be second-guessed, no matter what. That's football. More important is that everyone remains clearheaded about it. In every way.

What controversy?

Alex Smith: Was not available for comment. Will talk to the media Thursday.
Colin Kaepernick: "Alex has been great. Our relationship hasn't changed."
Jim Harbaugh: "Both have earned it. Colin has the hot hand. We'll go with Colin."