I'd let the dealership take care of it, but I'd nicely tell them that you'd like to take a quick look at it with a friend before they start. Then hire your friend, a reputable mechanic/repair person, to go with you to take pictures/notes. This is so that you know exactly what the damage is and can have a neutral 3rd party review the work. Keep the temp of the situation low and be sure to tell the dealer that you appreciate them 'fessing up and offering to take care of the damage. When you pick it up, when it is still at the dealer (IMPORTANT), have your friend come back with to review the work. At that point, you can tell the dealer that although you are a trusting person, you are a big fan of Ronald Reagan--Trust but Verify. At that point, you might ask if they would be willing to reimburse you for the 3rd party review. If you're nice, and the report is good, they may agree to do so. If your friend sees that the work is shoddy or incomplete, with the pictures, etc., your position with the dealer is much stronger. Good luck.
Ha! I didn't even answer your question. The answer, unfortunately, is yes, there will be diminished value and you would be very well within your rights to have an appraiser tell you the difference between a damaged, but fixed and undamaged cab-over. You could ask the dealer to reimburse you that amount. But be careful--if they ask you to sign something before starting the work, be sure you do not inadvertently release any rights you have re: the 3rd party report or the difference in value. Usual Disclaimer: Not legal advice.