What they might do is sell the contents of the destroyed premium packs, not sure if that's even allowed through their contract with Konami. They might auction off the damaged box sets as a complete packages, you might get a good deal if you are just after the steelbook or artbook....The games will probably go back up on the Zavvi site even though they aren't sealed.
Again I'm not sure of the legal issues here though.....Personally I hope they are forced to destroy them, it will lose those fucks money and make my two mint copies all the more rare