They have been playing without an NFL QB for years.
Alex Smith is replaceable, Peyton Manning is not
It is true that the Niners have been playing without an NFL-caliber starting quarterback for years.... ever since Garcia left. It is not true that they have been performing without one. Most years the Niners have been in the playoff hunt primarily because the NFC West has routinely sucked donkey balls. There have really been no flashes of brilliance. On occasion there was a flash of competency.
Every Thanksgiving for years I have looked at my nfl.com standings and told myself "If only my Niners can win the rest of their games..." and every time they have failed to even come close.
If I were handing out the League MVP award then it would have gone to Peyton Manning last year, primarily based on how his team performed. So I do agree that he's a much better QB than Smith, but I don't see Harbaugh and Manning meshing well at all. I don't see the Niners as being the kind of team that picks up has-beens. They're not the Jets.
The best move for the Niners right now would be to keep Smith and try again next year.