Without BFR Zoom has to ko Supes (not an easy task with his powerset). Supes should have advantages with his flight. He can heat up the whole battlefield area thereby burning/melting the battle field preventing Zoom from running effectively.
Or he can slow down Zooms kinetic energy in the air with his freeze powers (not likely to work if Zoom is accelerating but it can counter or impede Zoom for long enough for other powers to work. One good shot and Zoom is done. Id favor Supes more often than not.
EDIT: It should also be mentioned that Supes can track Zoom and has tagged him at least on one occassion that I know of. So instead of shooting precise beams of HV he'll probably just heat up the whole area.