I'm sorry this happened to you. Have you brought this up to the applicator? If he is a stand up guy he will make you whole again. It will not be cheap but he probably will not make that mistake again. If he tells you you got what you paid for then you have some choices to make. Was this guy a certified applicator? Just wondering as a few of the popular applicators on these forums are not certified and just do it how ever. If he is certified I would report him to NIC so he can be re-coached on the proper application of the product.
To determine how your barrel is I would pass a lead slug from the chamber through the bore to check for tight spots. I'm certain it will not get past the coating if it's really in there. If the lead slug passes it may shoot out. A borescope will reveal the extent of the damage from the aluminum oxide prep. If it's not roughed up it's won't stick for long and will blow right out. Eventually it will boil down to how does it shoot? If it was prepped right there is no way to remove it without causing more damage or just simply cutting it off. Go shoot it 30 or 40 times and see how it groups. If it's fouled up I would request he fund a new barrel. If he can't handle coating it right no way I would trust him to install a barrel.
Good luck and keep us posted how it all turns out.
Shawn