I'm curious if the boarding pass and receipt the kiosk spit out at you also had the class of service on it... did it say anything like 'business elite' or something for the fare like J/C/D/I/Z or OP? Any other things to suggest the BE cabin such as 'PREM' for boarding zone, or SkyPriority etc?

At a bare minimum you are obviously owed the miles back since DL took them for nothing. Oh and btw... officially miles upgrades aren't processed day of departure, however some gate agents can and will do it. I think you should also be given some additional miles for the trouble. Did you go from a decent seat to a crappy one in back?