If the shop told you about the insurance company's practices only after the problem came up, I think they are in the wrong, no matter what the document your wife signed might say (based on how you've described it).
If you had known that the shop wasn't going to take what the estimate said, you could have looked for another repair shop that would take the estimate. What that document says might be very important, though, and I'd suggest you have a lawyer read it and explain it to you, before you go to court to fight this.