Well, he was 60 feet away. Plus, the kid was hiding, not actively throwing anything. The coward shot a child that was not a threat.
"Fifteen-year-old Sergio ran past Mesa and hid behind a pillar beneath the bridge on the Mexican side. As the boy peeked out, Agent Mesa, 60 feet or so away on the U.S. side, drew his gun, aimed it at the boy, and fired three times, the last shot hitting the boy in the head."