It would be good to know how thorough their alternator belt check was. Hopefully it wasn't just a "Yeah that looks OK" job. The alternator pulley has a one way clutch on it, which if it fails, could potentially cause noise. If the pulleys look shiny on the inner ridges, that indicates a worn belt.
The only other thing I can think of that makes a loud squealing noise is the turbo. The turbo and exhaust manifold are one part, so they can check that when they've got it apart. £500-600 sounds steep to look for a broken bolt, and I'm not sure how that would cause a squealing noise, but if the turbo itself is shot, you're looking at £1000 + fitting for a brand new one. Refurbished ones usually cost around £500, which I would take over a £200 chinese one from ebay.
Good luck!