Eh, I don't subscribe to the "you don't lose your starting job because of injury" line of thought. You start whomever gives you the best chance to win. Kaepernick shredded a defense that had been pretty rock-solid this year (seriously, he just abused Major Wright all night long, and Tillman was just getting clowned on every passing down) and he pretty clearly has the team around him, as opposed to Smith, who still has his opponents within the team. Start Kaepernick until he fucks up.
While I agree, it's generally at least the starter's job to lose. Alex Smith wasn't playing close to poorly and they were winning games. I agree that Kaepernick has a better upside, but there's always a risk when you change players so you generally avoid it.
But we'll see how it ends up.