All the flame wars about whether or not Kaepernick is, in fact, a top-ten quarterback have shed a lot of heat but very little light on the subject of CK's next contract. It doesn't matter in the least whether Kaepernick is a top-ten quarterback.
Let me say that again. It doesn't matter whether or not Kaepernick is a top ten quarterback. It only matters what other GM's think about his capability or potential. They will set the price for his contract. If only one GM on a team struggling without a franchise quarterback thinks that he will be the answer for their team, that GM will set the negotiating price.
If you sincerely believe that no GM will compete for Kaepernick at a top ten price, then you can expect him to sign for $10M/year, without a squawk. If you believe, as I do, that there is a GM out there with a load of cap space and an empty hole where his franchise QB belongs, then you must expect that offer to be very substantial (I would guess $18-$22M/year).
From that price you can hope for a discount, based upon.
1. Kaepernick's desire to stay with the team
2. Kaepernick's desire to continue developing with Harbaugh
3. Kaepernick not wanting to spend his career in Cleveland (or Jacksonville, or gulp, Oakland).
4. Kaepernick wanting to preserve the ability of the team to surround him with quality players.
Once the discount (if any) is settled, the FO will have to make a decision. Either pay the man, or start looking for someone else. While it is true that we could probably post a decent record with a QB like McCown, I don't think we could plan any deep runs into the playoffs until we acquire a true franchise QB. That is a big setback, and one I wouldn't look forward to taking, especially with so many talented players at the peak of their careers on our current roster.
If the goal is to make the playoffs most years, then we could probably let Kap go, and keep shuttling new players in through the draft. If the goal is to win Superbowls, we are probably best off to find a way to afford CK.