The implication seems to be not that the station has multiple reactors (all signs point to it having a single main reactor) but that they're referring to the amount of energy output from the hypermatter reactor itself.
Note that they use a series of baffles to reduce the amount of radiation, and hence power being generated by the main reactor. This presumably is what they mean by using a single reactor.
“Target Jedha City,” he snapped. “Prepare single reactor ignition.”
Krennic concealed his resentment, calmed himself with the sounds of
his breath and the tidal rush of the station reactor. This wasn’t how
he’d imagined the culmination of twenty years’ work—a diminished
attack, a grand moff’s power play—but it was the reality he contended
KRENNIC PACED THE OVERBRIDGE UNDER Tarkin’s watch, observing the
technicians and referencing every step against the control protocols
he’d memorized long ago. Levers were flipped, rotating focusing lenses
deep within the station’s core. Engineers adjusted radiation baffles
and ventilation pumps as the main reactor shook with effort and its
comforting roar turned to an eerie scream. Krennic saw more than one
hand shaking, more than one face flushed or daubed with sweat. But his
officers knew their duty. They would do everything necessary to
destroy Jedha City at the bidding of their commander.
Rogue One: A Star Wars Story - Official novelisation