If it bothers you (as it would me) ... I'd have them do it and then make them work on it until it was perfect if need be. You have every right to a car that works properly without any self inflicted visible defects.
Good luck and I hope they fix it for you perfectly the first time !
Also, as another poster mentioned ... I'd think they could replace the whole door frame (or whatever was needed) with all new parts far cheaper than doing the kind of 'surgery' they're talking about.