I think I'd be really pissed if someone did that to my 406
I think that probably won't have any effect on the structure of the car (not that I have any experience or qualifications in this area). You could maybe push it out by drilling through the floor pan -but- as you say, it'll be messy. The proper way would be to cut it off, straighten it, and weld it back on (hideously costly and messy too). It'll also depend if the garage is admiring fault, if they're paying then the ball's in your court.
Other than that, I'd be concerned with the damage to rust-proofing, it won't effect integrate how it is but add a little rust...