After Naoi's taken control of the Student Council she starts using them as shields against the Battle Front because, as Yuri said, they can't attack NPCs.
I would get if it was a moral ground they stood but in the climax we see that a number of the guys following Naoi was holding guns. Sure they might not be able to be killed but it does seem dumb for them to hold back against combatants.
Is there a reason why the Battle Front can't fight armed NPCs?