There are a lot of things to consider though. Yes it's relatively easy to develop an offense to utilize his strengths, but it's not a temporary solution like you suggested. If you go to the lengths and labors to develop an offense tailored to one player, then you need that one player to be able to run it. What happens if he gets injured or just plain sucks? Now you need a backup QB of equal or similar skill set to keep the offense on track. You can't go from zone-read with Kaepernick to zone-read with, say, Sean Mannion. And if you remove the zone read elements from it to accommodate a different QB (like Mannion) who isn't capable of running zone-read as effectively, how much does that put on the offensive line and receivers? They essentially have to know two offenses. Or, alternatively, you have a very scaled back offense after you strip all the zone-read out of it.
See what I'm saying? It's not a good plan if you change the offense for the QB, RB, line and receivers, but don't plan on keeping that QB for very long or even know that he'll be productive in it. You'd have to have a couple of QBs who can run it if you're going to go in that direction. It's kind of a big deal to move in that direction, or all NFL coordinators would have a backup plan like that. Our offense isn't working? Well crap -- let's just do some zone-read and get Kaepernick or someone who's done that before and see if that works. If it doesn't, we can go back to what we were doing before. I mean, does that ever happen?