I think even before the season started Alonso was designated as the #1.
The decision to issue orders was probably reached on the pit wall @ Hockenheim. If the team had put together some kind of plan beforehand you would think they could of come up with something a little more clever then: "Fernando is faster then you. Did you understand that message?" Then again maybe Ferrari didn't give a shit and knew they would probably get away with it.
Obviously the decision has worked out well. Alonso has been on fire & Massa has been a mess. Massa can't really believe he'll be level with Alonso if he returns next season.