I agree that Alex Smith will not be a back up next season. Not on this team and not on any team. If he lands in Arizona, he's already better than Kolb or Skelton. He could also end up on a team like the Ravens (if Flacco isn't brought back), Jaguars, Jets or Chiefs. All of those teams need a starting QB.
You have to take into consideration the coaching past of Alex Smith. Different coaches and offensive coordinators in his first 5 years which really hindered his development. None of those coaches were "QB" coaches like Harbaugh either. Smith is also 28 years old and if developed correctly, would be in his prime of his career. Imagine if he had a coach like Harbaugh right off the bat instead of guys like Nolan and Singletary. What kind of QB would Smith be now? Drew Brees wasn't the Brees we all now know until he was 26 years old.
Handing the reigns over to Kaepernick, IMO, was a premature move that could come back and bite them in the *** in the playoffs and for the future.