If he comes back it will just be rinse and repeat next year. I'd also guess that one of the things that frosts Harbaugh about Manuel is that Warde wants to up Harbaugh's reverse buyout in any new deal to something pretty painful, (it was $2.5M to start in the last one, dropping to $1.5M this year) which might be one of the things beside the arbitration panel that is a sticking point.
A goofy idea, but with Harbaugh I think it's a possible one, is that I would not be surprised if Jim Harbaugh want's to wait to see if Jack Harbaugh gets to another SB and what the outcome is, while his suitors in the NFL might be demanding he decide before then..