I would just think you're out of luck if that's what your company negotiated. You could try mailing in your boarding passes after the flight for credit and see what happens, but this doesn't seem right being that you knew what the conditions were when the ticket was issued.

Do you have any workarounds (such as flying another carrier that might offer the same, or lower, fare)? That might seem your best option. Some flyers here have been able to get their companies to allow them to fly alternate carriers if they can beat the fare (or pay the difference if the fare is more). Might be worth looking at it from that angle instead.