I doubt Alex is going anywhere. I think it would fuck up the team chemistry if he dropped Alex after they made it to the NFC Championship (possibly Super Bowl) with him at QB
I still don't think Alex is a great QB, but he's been very solid this year.
The only reason for the Niners to get rid of Alex would be to get a QB that could win now, assuming they don't think Alex can get them a ring. There's really nobody out available to do that... unless Peyton Manning is healthy, and the Colts wanna trade him