Because there isnt five hundred faunas down there. There was five hundred before shit went down, and obviously things have changed since then. Remember, you're only getting one side of the story, and it doesnt always mean that you're getting the truth. If you really want the character to know what to do, they need to explore their options instead of just doing everything my NPC's tell you. Of course, killing the faunus would be the simple and quick way to finish the mission, if Team MODA feels that this has dragged on for too long. As always, the choice is yours.