Of course I don't know the back story, but I wonder if it might be the dealer rather than Guild who is at fault. One possible scenario (although, again, I don't know what actually happened) is that the fret ends were a bit sloppy and the dealer tried to clean them up, screwing up the binding in the process. I find it really hard to imagine something leaving the factory with that binding. Rough fret ends, perhaps, but not that binding. Installing fretboard binding isn't that tough. You just rout a channel, lay in some glue, run the strip of plastic binding along the groove, tape it place, let it dry, and trim things up a bit. It's body binding that can be a bear because of the difficulty of getting the mitered joins to be tight and clean.
Guild should be able to fix that guitar so that the binding looks as it should. Worst case is that they pull the frets, remove the original binding, rebind the board, and refret the guitar. For a factory, that's a piece of cake and there should be no sign that anything has been done when they're through. Geez, they're the freakin' factory. They could even re-neck the guitar if needed.
I agree that the back is exceptionally pretty and if the sound is also special, then getting that instrument put right should be your goal -- and it's not an unreasonable goal, at all.
I think you're wise not to mention the dealer until this gets resolved. Good will can be helpful in a situation like this. Both the factory and the dealer have an opportunity to make a favorable impression on a core group of potential customers by doing the right thing here. If being reasonable doesn't work, there's time for a more aggressive approach later. But I'd begin by appealing to their better nature. Personally, I'd be reluctant to take a discount without being absolutely sure that the difference in price was enough to cover fully the cost of replacing the neck binding. The factory should be able to do the binding repair as well or better than anyone else.
Finally, I just want to say how sorry I am that what should have been a good experience for you has turned into such a bummer. All I can say by way of encouragement is that I've seen other situations like this over the years that have had happy endings. It takes patience and forbearance, but these things can get worked out.