Seems to me that it certainly could happen that repair costs substantially exceed the initial estimate once a repair shop gets fully into the project - but to my way of thinking, that should be the only reason that they should legitimately be able to up the price, not because of their internal labour problems that have nothing to do with you.
As well if they force increasing the price that much, it seems totally unreasonable for them to proceed without them first discussing the situation with you and getting your ok,
If they did not do this, I would think you would have a good shot at getting the charges reduced in a small claims court environment (Although I don't have any personal experience in court cases.)
Brian & Connie Mitchell
2005 Classic 30'
Hensley Arrow / Centramatics
2008 GMC Sierra SLT 2500HD,4x4,Crew Cab, Diesel, Leer cap.