If you were looking to purchase a bass and discovered a visible full-pocket neck shim installed, how would that affect your interest level?IMO the body is not ruined and the neck can easily be brought back to the proper height by shimming it. Did he screw up? Yes! I would have him glue in a laminate piece in to the neck pocket to bring it back up to the proper height then put it all back together and set it up correctly, all at no charge or at least at a highly discounted rate! If he balks at that then demand he purchase you a replacement body.
I know it would be perfectly functional, but I would be compelled to pay much less for the bass than I would for the same bass without such an issue...or more likely just pass altogether.
The OP should not settle for anything other than a new body...I know it sounds harsh but that is the only way to set this straight. This is my opinion of course and if the OP wants to be forgiving and take the hit rather than the guy that made the mistake then that's their decision.