Don't assume the gate agent is aware of the delay on your scheduled flight. Many on FT monitor the inbound flight status as that can often indicate your flight will be delayed even if the monitor shows on-time. If your outbound will be delayed and the gate agent is still indicating you will need to pay the upgrade charge, ask for a supervisor. At one time, this accommodation was referred to as Rule 85 by WN, not sure if that is still the case.

(I had a instance, circa 1994, where SMF had horrible weather. I made a new reservation by phone and the phone agent advised me Rule 85 was in effect due to weather, that the flight I was making a reservation for might not go but that I might be accommodated on another flight.)