This may not be a contending team, but it's certainly not a rebuilding one either. If they can stay healthy and get decent play from the QB (big ifs), then they could surprise folks and win 7 or 8 games.
The mission statement for the 49ers is simple: show improvement from last year. That's it. They need to win as many games as they can, right now. Nolan and Martz are both fighting to salvage their NFL coaching careers. They need to play whichever QB gives them the best chance to win, and could care less about nurturing Alex's future. But if Alex ever does catch up and prove himself more capable in this offense than JTO, then I'm sure Martz will be happy to plug him in.
But my point is, I don't care who the QB is. The Alex Soap Opera was last year's story. The big issue right now is seeing the coaching staff get the most out of this team's talent.