Well, I'm speaking from a contractor's point of view here as I work for a builder. Normally the builder installs the appliances at no charge, into the openings provided. This means that if you contracted with a cabinet company, it was their responsibility to obtain the "specs" on the appliances you selected and make sure the openings were the right size. Personally, I don't see the contractor giving you any credit for something that was beyond their control, unless when you say contractor, this means that your contractor was responsible for the cabinets and then it would fall within his realm of responsibility and he should be willing to give you a credit towards the damage. I don't think you stand much of a change of getting them to completely replace it. If the contractor was responsible for the openings, your other alternative is to go ahead and buy a new refrigerator, have it installed and then take the contractor to small claims Court (since it's less than $3,000 - but check on the jurisdiction in your courts) and resolve it that way.
Also, normally when you sell a house, you leave the appliances and it would be very unusual to take the refrigerator with you, unless it is a second refrigerator, so you wouldn't need to worry about it showing in the future.
Next, you should be forewarned that should you hold back and refuse to make full payment, the contractor can simply file a Mechanic's Lien against the property. This would then force you to incur legal costs if you decide to refinance or move.
The easiest thing it to talk to the contractor and see what you can get out of them. You never know what they may be willing to do unless you approach them. They aren't going to offer anything without your bringing to their attention.
Good Luck!
Please post how you ultimately resolve it.