Is it possible to specify whether a recipe should use damaged or undamaged ingredients somehow? So for example you could make a repair bench that only accepts damaged items and which in turn spits out fixed items.
Maybe, I'd dig into ThingFilter and possibly its specialFilters. But, my guess would be no and since ThingFilter is yet another non-virtual without an interface, you'd be hard-pressed to monkey-patch filtration. I was just looking at it as a way to filter by size and decided to heck with it.
I can't think of an easy way to make it work without, probably, a lot of coding. In theory adding a couple of lines to the WorkGiver_DoBill to filter out damaged ingredients may work. But it's a complex workgiver, the more I look at the code the less I think it's a good idea. I'm not sure.
I don't think it's possible... at least I couldn't find a way to do it.
If you want a repair bench, though, I just released one in the mods forum (Mending mod).