[Isterio]

Originally Posted by WabbitTwaks

I think it comes down to how his son is involved in the two situations.

When he was trying to protect his son. That warrants shooting. No hesitation. Kill them before they kill Shawn.

Later, in the comic, his son has turned. In Hershel's mind, by some miracle his son is alive again. He thinks, "Maybe everyone else is just sick too?" So now he views anyone with the same "disease" as Shawn, as alive, and possibly curable. He believes, "If they can be cured, you shouldn't be killing them."

You might be right