Nunnaly might die in the nuke explosion.
Think of this senario: The Knights attack, and the gefjun disturber is activated, halting a very large percentage of the Britannian forces in their tracks, allowing for a slaughter. Schnizel needs to deal with the situation immediately, and orders Suzaku to nuke the power plant in order to cut off the power to the disturbers before his entire army is wiped out.
Unleashing the nuke will lead to the deaths of thousands of innocents, and Suzaku is reluctant to do it. Schnizel tells him that he either complies with his order or is shot to hell. We now have a repeat of the situation from season 1 where Suzaku was told to shoot Lelouch and refused, accepting death so that he didn't have to shoot his friend and do something he didn't want to.
But he can't accept death this time.
His Live geass activates, and he launches the nuke, kills thousands of people and now hates both himself and Lelouch eternally.