Obviously, I hope the Niners do fork over the money but in this case, I think the team may have more leverage than the player. Harbaugh's got them the the NFCC game with Smith and Kaepernick so I think it would be very easy for them to just move on. CK hasn't exactly come up big with his arm and that's what QB's get paid for.
I think he'll get a raise but overall, I don't think the 49ers will have to negotiate out of fear like most teams do when a QB emerges. Seattle's in a lot tougher spot when it comes to Wilson's contract. Even though that team is designed much the same way, Wilson has put them over the top.