If you have any
pictures of how the frame looked before it went off for repair, then make sure you have them to hand. Take pictures of the frame as it is in it's current state (ie. after it's been repaired). Might be worth putting a copy of today's newspaper next to it so they can see that the pictures are recent.
Get in touch with the repair company (as has been mentioned before, aim for a manager), and say that you have before/after pictures and can prove that the damage was done whilst the frame was in their possession.
Explain that you, as their customer, are well within your rights to expect to have the frame returned to you in the same condition cosmetically as it was sent to them. Get some decals priced up from Gil and ask the repair company to refinish the frame, apply the new decals and re-laquer.
I had the exact same problem with an Intense M1 frame a few years ago. As soon as I was able to prove that they
did the damage, they re-stripped and re-sprayed the frame.