OP, you got totally hosed, and I will also call Shenanigans on this one by the GA.
Absolutely, definitely, 100% call and write to Delta about this. It is unacceptable that they did not follow SWU airport standby procedure. As a DM using an SWU on a B fare, you would certainly be in the top couple on the list. The proper upgrade list was obviously ignored by the GA and they provided op-up to inappropriate pax. If it can be confirmed that there were NRSA given op-up ahead of you, then that is grounds for termination.
Its extremely upsetting and unfortunately, but JFK seems to be among the worst locations for GAs ignoring the rules for things like this.