The difference between a deluxe and a standard is more than the size of the neck pocket. Sure, you can take a standard body and route it for a deluxe neck but it would still be a mismatch. J & P Deluxe basses are clearly listed as incompatible on their site. So you made the mistake by ordering an incompatible body and they stuck to their guns on their written cancellation policy. Who knows how far along your order was by the time you cancelled? It may very well have cost them time and resources.
The situation does suck, I would be upset too. It may have been nice for them to waive the fee, but it's not wrong that they didn't.