Harbaugh's three options at quarterback

Colin Kaepernick did his part Monday night to create a healthy quarterback debate. And coach Jim Harbaugh added a little fuel to the discussion when he refused to say those words he had said so many times when there was even a sliver of doubt.But Harbaugh did not say, "Alex is our guy." And that is important to note.So now there's an honest-to-goodness quarterback decision that faces Harbaugh and his coaching staff. There was no debate until Monday night. But Kaepernick's exceptional play forced the issue.And, right now, there can be no quarterback controversy until there are two healthy quarterbacks. Alex Smith must first be medically cleared to play before there's any true debate within the 49ers' coaching ranks.Smith was cleared to practice last week. And he went through multiple normal days of practices until, apparently, some concussion symptoms presented themselves over the weekend.Kaepernick did not get the full week of practice, as would be expected for any starting quarterback. But he made it a moot point. Kaepernick was outstanding in the 49ers' 32-7 victory over the Chicago Bears.Here are the three options Harbaugh must consider:This week, Kaepernick starts: This is the equivalent of deferring the real decision until a later date.In order to give the 49ers' starting quarterback all the reps during a week of practice to face a surging Saints team, Harbaugh could declare that Kaepernick will start Sunday against the Saints. This decision would be made because of the uncertainty of Smith's condition."It looks like he will be (cleared) before the week is out," Harbaugh said Wednesday morning on KNBR's Murph and Mac Show. "But not as of now. I'm sure he will be."Harbaugh could take the stance that he does not want to get stuck in a situation similar to last week. It would prevent the possibility of Smith taking the majority of the practice time and then not being well enough to play. If Smith experiences any symptoms after the flight to New Orleans, he would not receive final clearance to play against the Saints.If the 49ers declare Kaepernick as the starter for this game only, it would give the team another sample from which to base their ultimate decision of which quarterback starts Dec. 2 at St. Louis . . . and for the remainder of the season.Long term, Smith starts: With Harbaugh's statement that he usually goes with the "hot hand," it's easy to forget just how hot Smith was before he exited the 49ers lineup Nov. 11 with a concussion.In his past two games, Smith completed 25 of 27 passes for 304 yards with four touchdowns, no interceptions, and a passer rating of 153.2. He was named NFC Offensive Player of the Week for his Oct. 29 performance against the Arizona Cardinals.The 49ers are 20-6 since the beginning of 2011 in games in which Smith started (not including the tie against the St. Louis Rams).Smith won the job convincingly in the offseason. And he is having far-and-away the best season statistically of his career. Smith's passer rating of 104.1 ranks third in the league behind Aaron Rodgers and Peyton Manning. He leads the NFL with a 70.0 completion percentage.Long term, Kaepernick starts: He made throws Monday night that Smith would not even attempt. Not only did Kaepernick throw those passes, he delivered them on the money -- repeatedly. The offense did not stall early. It looked explosive and impressive.Kaepernick pushed the ball down the field. He got tight end Vernon Davis involved from the beginning of the game. And he made a fourth-quarter throw to Davis between two defenders that Davis said looked like something he would see from Tom Brady.Kaepernick also seemed to have a very good handle on all of his responsibilities at the line of scrimmage. Harbaugh said after the game he could think of only one pre-snap misread. Kaepernick seemed to regularly get the 49ers into plays -- run and pass -- that were successful against what he saw from the Bears' defense.The 49ers' practices have been closed to the media since midway through the exhibition season. Up to that point, Kaepernick did not demonstrate the kind of accuracy one would expect from a starter.But, clearly, Kaepernick has gained a better understanding of the offensive system. It looked as if the game was coming easy to him Monday night. If he's more comfortable, it is going to be reflected in the accuracy of his throws.If Kaepernick has been practicing like he played Monday night, then this could be the long-term call for the 49ers' coaching staff.