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John Locke had to go through everything he did (go off the island, die, come back) so that he could come back to help Jacob... by killing him. Why kill him, i don't know but Jacob said "Help Me" to John very clearly and only John Heard it. Ever since then, he's seen Christian Shephard twice, who speaks on Jacob's behalf. Shepherd told him to do what he did, that he had to die etc. Christian Shepherd is part of the Island. He told Michael "He could go now" right before he died. He knows whats going on on the island and speaks for Jacob. Maybe Richard and Ben were using Jacob, or just using the notion of Jacob, to exploit various things. But for whatever reason, John has been long destined to come to the Island and fulfill his prophecy. He now is spoken to by the Island, he knew exactly when to find his time-traveling self because the Island told him. He is now the one most connected with the island, bear in mind he was a corpse coming to the island which can have different effects (ex. Christian Shepherd). I think Locke is meant to take control of the Others and "help" Jacob. Jacob is definitely real and essentially one with the Island, which is now making John Locke a prophet of sorts. I don't know why he has to kill him though. However, it is obvious that John is the most important person to the island right now. John has been following a path since he's been getting dreams. Horace appeared to John in a dream where he was building Jacob's Cabin. He told John that Jacob was waiting for him for a long time and that he had to find him(Horace) and then find Jacob. He found Horace's body with the Cabin map in it, etc.
As far as what Richard said about Locke being a problem: I think that he just meant he's moving to fast, not being discrete, and radically taking a lot of people to see Jacob on his first day. Plus, you can't stop John Locke, you can't kill him. Also, Richard doesn't know nearly as much as previously thought. He's just concerned about what Locke's doing with his people that he's been with for a long time. Richard and Ben seem to be on the same page, bear in mind Richard basically brought Ben in to the Others as a kid. What if he was never really meant to lead them and he's never seen Jacob, like Locke said. Or if Richard and Ben have their own agenda? Either way I trust Locke.
PS whatever Jack and them are trying to do is bullshit. The bomb won't be detonated, that's just ridiculous. It would kill off so many people in their own present time and change so many things drastically. Why does it just matter that Jack and them have their old lives? Jack was miserable back in the real world. I don't see why Eloise and Richard are going along with this. *Also, Sayid coming out of the bushes and pwning was hilarious.