Why can't the Battle Front fight NPCs?
As I get it, it is just part of their moral code never to fight innocents including NPCs. I don't know why but they say "must not" so it has to be a rule and it is the SSS so it can't be a "Word of God".

There is (as far as I know the anime and the fan wiki) no canon explanation. Maybe they give respect for the possibility of real AIs or that they can't be 100% sure not to missjudge a human for an NPC.

When the Shadows appeard, they had no problem fighting this mutated NPCs but at this point, they could be sure not to deal with a human like consciousness or a real human.