So, first off mistakes happen. It was probably a screw on the floor of the shop that the tire picked up (it looks like a trim screw). Had they noticed it before you, I guarantee that they would have fixed the tire with a plug and patch and you'd never had known the difference. I'd have them plug and patch the tire, which is a proper repair for this type of damage, and give you free, or at least a discount, on the tire installation. Having a screw stuck in the tread (are you sure it punctured the tire carcass?) and properly repaired is not going to degrade the performance, longevity, or reliability of the tire.
As far as the rims, well thatís a different issue. Believe me, the rims will not look new in a few months or years, so Iím not sure why it will be an issue for you. The rims are going to get scratched at some point, trust me on that.