Really cool twist. Something about playing as a machine made me assume when the game started that the point was to save anyone I could. It didn't occur to me what was really going on until I found out in-game.
One thing that could have been cool would be finding ways to reveal a little more about the surviving crew member; if there's something of a bond that the player makes with him/her over the short time they spend together I think it would make deciding on whether to succeed at your programmed directive a much more difficult and bittersweet choice.
It's a good IF, I like how it manages to tell an interesting story with such a minimal script.