Is the more expensive shop charging YOU for shipping the bent into his inventory? For some bikes it adds up to $300-$400 MORE than ordering one on the internet from Calhoun or Hostelshoppe! I think this is wrong..the business should be able to absorb some of that, unless it's really struggling. Of maybe the prices went up from last year.
Anyway, ask them WHY the higher charge and then see if they'll come down to meet the price of the other shop. Also, to add, I'd go with the shop where I felt more comfortable and had a good rapport with the shop owner and wrenches. That is something you'll need down the road as well.