Your post doesn't state categorically that they actually did the repair. Did they? What proof did they provide? Actually, I don't think it really matters whether they did or not. I'm not a lawyer, but it seems to me that the repair isn't complete until they deliver the unit back to you in verified working order. Their insurance would probably reimburse them for both the cost of the laptop plus the lost revenue for the repair (plus the cost of everything else that was stolen). I'll bet they're double-dipping, trying to hose you as well as collect from their insurance company. Consider this; let's say you bought something at Amazon and it never came. Now, you contact Amazon and they say, "Well, sir, since we did send it to you, we're not going to refund your money. It's not our fault it never reached you. If it was stolen (from us, not from you), we'll be happy to refund you your money, minus the full cost of the unit, which we did ship, so you get bupkes. Have a nice day!" Does that make any sense? I think not.
As someone already mentioned, if you had software on the laptop, the cost of software (if you don't have the keys stored anywhere else) could be greater than the cost of the laptop. What about the value of your data (I hope you backed everything up)?
I realize that the world is already too litigious, but if you want to get an idea of what you should be entitled to, consider putting up a free post at findlaw.com. It's really not enough money to involve a lawyer, but that's what small claims court is for. If they're incorporated, they'll probably need a lawyer to defend them, but you won't. It will probably be cheaper for them to give you a brand new laptop rather than pay their lawyer thousands. Personally, I think you deserve a replacement, plus retribution for the runaround, plus damages for their sleaziness.