Unfortunately, you only earn miles and points for the originally purchased price when you upgrade with instruments, miles and copayment,
Load Factor Based Upgrade (upgrade offered when checking in online, at kiosk or counter), etc.
If you paid money to exchange an Economy to Business or First ticket, you should earn at the newly purchased class of service. If you were offered a LFBU, you would earn at the originally purchased price.
If not an LFBU, you might call once more and ask to speak to a supervisor, and see if your ticket booked as an upgrade or purchased ticket - if Business, I, D, J; if First, P, A, F. But it looks like you were offered a LFBU. A good deal, indeed, even with the original miles earned.
See
GUIDE: Help Understanding Status, Points / Miles & Segments: EQM vs EQP (merged thd.).
This thread will be merged soon.