Not really much of a theory as it is pointing out something I noticed rewatching season 5 at the beginning. So Jack put's his dad's shoes on John Locke before he goes back to the island. Which is fine and makes sense at first.
It is assumed that upon arriving at the island, the Smoke monster or MIB (both maybe if they are the same one) tucked John Locke's body into that trunk and assumed John's identity. Well I got to thinking that what if at the end of the season Jacob is just assuming that MIB has assumed Locke's identity. But what I am thinking is that John did revive upon arriving at the island, that whatever Jacob did when he first revived him after falling from the window, it pretty much helps John to heal faster on the island..or in this case, come back to life.
So what I am getting at is this. MIB expected to find a dead John Locke in the casket in the cargo hold when the plane crashed, so he marched up to assume his identity, but when he arrived, he finds a very confused and much alive John Locke. So MIB and Locke exchange words, Locke learns his intentions, MIB attempts to convince John that Jacob must die. Locke listens and either decides he's heard enough and kills the clone, or he ends up killing it in self defense.
So John knowing this will create some confusion, tucks the extra "Locke" away to keep the other wreck survivors from finding it easily, as he knows it's gonna be tough from here on hout. The reason I believe that it's the real John Locke that convinces Ben to kill Jacob? All because of those shoes that Jack put on Locke before they left to come back. At the beginning of "the Life and Death of Jeremy Bentham" After the scene where he is shown sitting in front of the campfire, it flashes to the next day. It shows on the beach near where he is standing the robe he had on the night before as well as the shoes Jack had put on him. As if he just had took them off.
After seeing that he was still wearing those shoes, I got to thinking that maybe, just maybe it was really Locke and whatever MIB said to him, convinced him that he really needed to kill Jacob. But Locke, not being a murderer (he was unable to kill his father, remember) had to find someone he knew would do it, that being Ben. So when they arrive, Jacob thinks it's MIB, cause why else would Locke wanna kill him. But in truth, it's just Locke.
It may be far fetched, but it seems really odd that one of the first scenes in "the Life and Death of Jeremy Bentham" actually shows the shoes sitting on the beach..as if they was dropping a big hint. Coarse MIB may have stole the shoes too, but I don't know if he would've been that thorough. Anyways, can't wait till season 6.