Yeah, put me down as believing that "Dead is Dead" John is now the same as Christian, a reincarnated physical vision.
I think that maybe the only person who has true free will to change the future is the leader of the Others ("The Variable"
) Jacob can't control what the leader does, only suggest. (Remember Christian told John he couldn't actually help him, that John had to do things for himself.) But when Ben came to power (imprisoning Jacob in the cabin with the ring of (sulfur?)), he stopped doing Jacob's bidding. Off-island Charles already knew about John as someone chosen by Jacob, so he manipulates events to get John on flight 815 and land on the island. When Ben takes John to Jacob, it's Jacob's chance for help.
Ben has never seen anyone dead be reincarnated (but we have). So when Ben tells John he wants to be judged for allowing Alex to be killed -- which is hardly the worst thing Ben has ever done -- then Smokey/John uses the "judgement ruse" to trick Ben into doing everything the new John says (thus getting Ben back to doing the bidding of Jacob/the Island). Smokey appears to Ben in the only form Ben might listen to, Alex. But, to me, Smokey, Alex, new John, Jacob, Christian, the Island are all the same entity.
Don't think Ben's promise to do everything John says will take, though.
