But that's the point: Herschel saw the truth: the teenager was not some warrior, and he sure as hell was not Martinez or the Bowman.
No, he saw what he wanted
to see; a defenseless, innocent young kid surrendering. But that's not what that combatant
was doing, despite running away. It was painfully clear -- painfully
clear -- that he was going to pull something. And even if he wasn't and was just being stupid, well, that's what happens to Stupid(tm) when in a warzone.
All he had to do was drop his weapon like he was ordered and he likely would have lived. Sure, Carl might have still shot him since he didn't have any means of securing a prisoner, but at least then
Hershel would have something to back up his sob story.