This happens more often than people would assume... It's not big deal. the bags aren't even ruined, honestly.
Take a small rectangular piece of sheet aluminum, large enough to cover the hole, and rivet it into place. Think of it like a patch for your pants, only made of metal...cause your pants are so badass.
Joe Bielski did this a few years ago and from what I remember it held up quite nicely. With the aluminum patch he was even able to leave the bags touching the pipes and didn't have much of an issue with heat getting into the bags either.
That being said, it wasn't your install and someone else messed it up. You can take it by there to appease the wife - they're going to tell you that once the bike leaves the shop they aren't liable for damage. But maybe you'll get a different answer. At least you can tell her you tried and then fix it on your own and everyone is happy.
