I agree with this yeah. If they settle on Kaepernick, Smith won't stick around, and if they go with Smith, Kaepernick won't want to stay, as Smith is too young for this to be a Favre/Rodgers type situation. Besides, who would be willing to hold a clipboard behind Alex Smith when they can clearly perform? Fuck that.
All the same, it remains to be seen if Alex Smith will have the physical skills three or four years from now to take the 49ers anywhere. He wasn't all that great to begin with. Further, he is injury prone; prior to last season, he had only played one full season, missing anywhere from 5-9 games in the others, and now he's back on the bench. With a history like that, and with Kaepernick's modest contract (three years left on a $5 million contract with $3.8 guaranteed), they can afford to wait it out. The problem with waiting is that Kaepernick might not get another chance to play again more than once or twice over the course of his contract, assuming the miraculous happens and Smith strings together a couple of 16 game seasons. By that point, Kaepernick will not be the commodity he is today, regardless of his skill set. It's a tricky situation to be in, but could be very beneficial if handled properly.