Shulk is against killing homs. Yet you can still fight and defeat Face Prototypes after the reveal. The item you get for beating them? Something like Bloody Face with the description of lives lost in the horrors of war. Despite Shulks moral stance he's still forced to kill his fellow homs in normal gameplay. A more powerful one in the Mechonis Factory even seems to have a name. And even if the player neglects to fight these enemies, the protagonists still unknowingly murdered the shit out of Xord earlier on in the game.