Make them fix anything they screwed up and then make sure you have something in writing that explains and admits their fvck up. Try to get them to warranty whatever you can in writing. I don't know how much success you'll have here.
If you have a good dealer, you might consider talking to someone there about the implications. Maybe you can have the dealer fix it and get the idiot shop to pay for it. Though, I don't think that is a reasonable option until the shop has a chance to fix their mistake.