His reward? Having recovered from a concussion, Smith is now No. 2 to Kaepernick, a second-year player from Nevada.
So the tricky issue for Smith's fans is that they have to hope Kaepernick fails although not to the degree of losing games and jeopardizing the 49ers' playoff seeding.
The trouble is, this guy really can play, as anyone who watched him shred the defenses of BYU and Utah State in 2010 should remember. Kaepernick likely will continue to thrive with the 49ers while Smith witnesses the unfolding of the latest episode of Things That Could Happen Only to Alex.
As it turns out, being yanked in and out of the lineup, playing for four head coaches and seven offensive coordinators, missing an entire season with a shoulder injury and losing all kinds of games may be only the preliminary events to the greatest cruelty Smith has suffered in San Francisco.
He's 19-5-1 as a starter in regular-season games under Harbaugh, he's completing 70 percent of his passes, and he'll be on the bench Sunday at St. Louis. Harbaugh's decision is not wrong, necessarily. It is justifiable. But it's unfair to Smith, and certainly plays into the story of his career.
"It's tough," Smith said. "You state your case with your play. … I feel like the only thing I did to lose my job was get a concussion."
Smith is handling his demotion both gracefully and honestly, registering his dissatisfaction without becoming a distraction. He'll be ready to perform as soon as his next opportunity comes but who knows when and where that will be?
Kaepernick just might seize control of this thing, judging by the way he played in a 32-7 victory over Chicago in his first start and followed with a 31-21 defeat of New Orleans, with the help of two defensive touchdowns. Obviously, Smith would love to be involved in a Super Bowl, but not actually playing in the game would serve as its own form of punishment.
Maybe it was asking too much to have Smith's breakthrough season of 2011 extend all the way to the Super Bowl, rather than end with an overtime loss to the New York Giants in the NFC championship game. But this year, Smith and the 49ers were nicely positioning themselves for another postseason run. He was expanding his game in the second season under Harbaugh and offensive coordinator Greg Roman, just as he did in the second year with Urban Meyer, Mike Sanford and Dan Mullen at Utah.
Over five quarters against Arizona and St. Louis, Smith completed 25 of 27 passes for 304 yards and four touchdowns. But he then took a hit to the head while scrambling, eventually leaving the game. Ruled out of the next contest vs. Chicago, Smith watched Kaepernick perform wonderfully.
So he understands why Harbaugh would make the switch, but he doesn't have to agree with it. That's the proper response to another adverse situation. Smith deals well with stuff like this, having gone through so much of it.
That's precisely the problem, in the cursed career of Alexander D. Smith. As always, he deserves better.