There is no denying how good Kaepernick was in his first NFL start, but Smith has shown he can work well in Harbaugh's system.
Sports Illustrated's Jim Trotter tweeted on Wednesday that Harbaugh has picked Kaepernick to start this week on a decision that was not based on health.
BREAKING: Jim Harbaugh has informed Alex Smith that Colin Kaepernick will start Sunday, per source. Said decision not based on health.— Jim Trotter (@SI_JimTrotter) November 22, 2012
Let's not get carried away by one game. Kaepernick did not turn the ball over against a great Chicago Bears defense and led the team to a blowout victory. However, a quarterback shouldn't lose his job due to an injury. Could this be another Drew Bledsoe-Tom Brady situation?
The 49ers are 20-6-1 in the last two seasons when Alex Smith has been the starter. The defense has been a big reason why the team has been so good, but the quarterback has learned to be efficient.
Who should be the 49ers' quarterback?
Smith has only thrown 10 interceptions in the past two years, which has been the key with a dominant defense. He avoids making mistakes that puts his defense in a tough spot.
It was only a few weeks ago when he had only one incompletion in a full game, and he has only had one game this year in which he did not complete at least 60 percent of his passes. That's getting the job done.
Don't forget that Smith led this team to the NFC title game last season with very little help from the wide receivers. With a loaded backfield and more talent in the receiving corps, Smith now has the talent around him to reach a Super Bowl.
While Kaepernick has the potential to run the football and make explosive plays, Smith is the safer bet. He will not turn the ball over very often or take unnecessary risks.
He had one terrible game against the New York Giants this season, but he has been solid in every other game.
Smith has done too much in the last 27 games to be benched after one good game by Kaepernick.
The only reason Kaepernick got a shot was because Smith suffered a concussion two weeks ago. If Smith is still feeling the effects of the injury, don't rush him back. Head injuries are serious and should be handled properly. Keep him out until he is completely healthy and then hand him his job back.
San Francisco leads its division and can make the playoffs with Kaepernick under center. However, the team needs someone who can make smart decisions in the playoffs.
Smith has proved himself in the playoffs, as he threw for almost 500 yards, five touchdowns and no interceptions in two games last postseason.
While the story of Kaepernick has been nice, Smith has done nothing to lose his job. The 49ers were 6-2 before his injury, and Smith has been one of the top-rated passers in the NFL in 2012.
As long as Smith is healthy, the job should be his until he proves otherwise.