Colin Kaepernick has accomplished in five starts what Alex Smith couldn't do in eight years: he threw for four touchdowns in a single game. Add in his 4-1 record as a starter along with passer ratings above 100 in three of his five starts, and Kaepernick has essentially locked up the starting quarterback role.
So barring injury or some bizarre meltdown, Kaepernick is the clear choice going forward. Alex Smith loyalists may be upset along with opposing defenses, but the controversy is a moot point now. Along with being able to throw the long ball, Kaepernick can beat opponents with his legs, averaging more than seven yards per carry on the season.
So what will happen to Alex Smith? Some desperate, bottom-feeder teams may cough up a late-round draft pick for him (e.g. Kansas City, Jacksonville, etc.), or the 49ers may just elect to cut him if they can't find an interested suitor.
Parting ways with Smith would certainly save the 49ers much needed cap space (over $8 million) and provide room to re-sign valuable free agents like Dashon Goldson, but Smith loyalists probably don't care much about that.
In their mind, Smith deserved to retain the job and probably should still have the starting job because of how long he'd been on the roster or how much he'd improved. With the Smith loyalists, it's about precedent, seniority and unwritten rules about not losing a job due to injury.
Obviously, that's not how 49ers coach Jim Harbaugh sees the football world. In Harbaugh's world, only the very best players take the field for his team, and that's to ensure the best chance of victory.
Now that Kaepernick has demonstrated through five games what Alex Smith couldn't do in eight years, the switch is permanent. The controversy is over. It's time for Smith's loyalists to either embrace the change to Kaepernick or risk being left behind.