The first shot may or may not have been accidental, caused by Arbery struggling to get the gun. Judging from the tape it could well have been. But McMichael had control enough to work the pump twice and pull the trigger twice. That's where the murder conviction may come from.
He's not charged with "murder"...he's charged with "aggravated assault" and "felony murder" which, if I understand it correctly, means (felony murder, that is) that a death was caused during the commission of a felony.
It's going to be hard to prove that Travis McMichael was committing a felony when Arbery ran at him.