I've certainly entertained the possibility of the Ordo Veritatis being a not so honest organization in the context of that game. They have a ''We are The Technocracy'' vibe about them that seems off for a ''we are the good guys'' faction.
And I really dig your 3 point as a game device for replay value! it kind of made me think of what an organization like NERV could do to people other than teens :D