Riza knows exactly what a bullet can do to a human skull. Ishbal was, after all, a crash course in terminal ballistics, and those lessons on velocity, calibre, and range have stayed with her when other memories have faded. After the war, even Hughes was never her equal at reading a crime scene when firearms were involved. He might not have been an innocent either, but he still lacked her special expertise.
Riza also knows precisely what this particular bullet will do to this particular skull, because she's taken this shot a hundred times in her nightmares. She has killed Roy at his desk in military HQ, surrounded by his stacks of neglected paperwork. In her father's study, as he traces patterns of salamanders and flame. On the bloody sands of Ishbal, surrounded by the wreckage of his own making. At Madame Christmas's bar, on the streets of East City, and in her rumpled bed. Only the most important details never change. Short range, her service handgun, and a head shot. It is always an execution.
Edward is shouting now, protecting Envy within his automail hand, and Riza wishes her own arms were made of steel. They would be steadier then. Roy is snarling back at Ed and Scar. He is giving her no reason to lower her gun and all the time in the world to fortify her resolve.
At Ishbal, she did the unthinkable on a daily basis; surely she can do it again. She can pull the trigger and watch him shatter. There was always the chance that this might be her final duty as his subordinate. That was the agreement from the beginning.
When the reprieve comes, she is the most surprised of any of them; she never believed in her heart of hearts that she deserved one. Roy pushes down her gun and apologizes, and only then does she let herself go limp with relief. She kneels on the ground, and shuts her eyes in a desperate attempt to regain her composure. The fight isn't over yet.
But this time when she opens her eyes, she won't have to hope it is morning.