vehicle was not damaged before you took possession of the rental. Tell them that you will be disputing the charge. I would not involved your insurance company yet - if you rented with a credit card that has primary car rental insurance you can file a claim through them.
They are probably trying to charge you for the lost revenue while the car was in the shop - rental car companies are really pinched for inventory now and are doing everything they can to maximize revenue.
(I just had the same thing happen to me on a smaller scale - rented a car in Hawaii over the summer, and 2 weeks after returning it I got a letter that they were charging me $250 because of "excessive sand" in the vehicle. I demanded photographic proof along with their written definition of excessive sand and they dropped it.)