Ever since Ben stabbed Jacob we have been led to believe that Ben never met Jacob before or even knew anything of Jacob's plans. That all this time Ben had been lying about everything in order to maintain his power as the leader of the Others. But I think this is wrong. I believe that Ben did know Jacob and in fact Jacob secretly set up a plan with Ben to murder him in order to put everyone one in the dark so that Ben could move like a secret agent through out both camps. It's sort of like how Dumbledore hatched his own death with Snape in that Snape was the one who "killed" him so that Snape could be a secret agent for the good guys.
The clues as to Ben being on Jacob's side are as follows;
1. We've been hearing all season that you can't kill MIB or Jacob if you let either one talk to you first before you stab them. And yet Jacob talked to Ben first before Ben stabbed him and Ben's knife was still able to do the deed. How is this possible? Could it be that Jacob allowed Ben to stab him?
2. If Ben has always been out of the loop, how did he know about the rules" when he said after Alex had been shot, "He changed the rules?"
3. We've been hearing that the reason Ben killed Jacob was because Jacob's wishes led to Alex's death as well as Ben losing his role as the Others' leader. However, it had been three years since Alex's death and Ben giving up leadership to Locke since he met Jacob under the foot. As we've seen the moment Ben jumped to Tunisia, he hasn't exactly been out of power. As he told Miles, he still commanded people off the Island as well as have millions of dollars just sitting around at his disposal. Ben still has power. He may not have been leader of the people on the Island but off the Island he could still get people to do what he wanted, so much so that he was able to find a way to walk right into Widmore's bedroom in the middle of the night and threaten him.
If he was truly fed up with Jacob as he seemed to be, why did he continue to do his work off the Island? Why not say, "Frak this. You cost me my job and my daughter, Jacob. I quit!" the moment he jumped to regular world and go and live on his own private island? Again, he had the power and the money.
A hint to the reason for this is given in the flashsideways between Dr. Ben and the principal. If we think of the principal as a Jacob figure than the first conversation they have outside the classroom takes on a whole knew meaning;
When the flashsideways start, Ben is talking about Napoleon, which is a nod to what had happened to Ben in the real world. Then Reynolds comes and tells Ben that he has been rescheduled.;
REYNOLDS: Linus, there is slight schedule shift. I am going to need you to supervise after school detention today.
BEN: What?
REYNOLDS: In fact, all week. Cut backs, budget crisis, events about your pay grade. Needless to say, some of us around going to have pull double duty.
BEN: We have history club today. Those kids need me.
REYNOLDS: There are five students in history club, Linus. They'll live.
BEN: Shouldn't we be encouraging the ones with ambition?
REYNOLDS: Spare me. The club isn't for them. It's for you. It makes you feel needed. Unfortunately, for now you're needed...in detention. Thanks for your understanding, Linus.
BEN: ...It's 'Doctor' Linus, actually.
Now if the theory is true, that the flashsideways is a glimpse of the real world plot, then you can suggest that Reynolds is Jacob and History Club is The Others, namely Otherton. Ben is looking after Otherton just like Alt!Ben is looking after the History Club. And here comes Jacob telling him that he's needed else where like Reynolds telling Alt!Ben he is needed in detention. (Funny how off the Island, Ben watched over the Oceanic 6 like a hawk as if he were in detention. He even said to Sun and Jack that they had no idea what he has been through to protect them.) Ben doesn't want to leave the Island. He thinks he is needed as Other leader. Jacob tells him that the Otherton leader was more for his own benefit. The Others will be fine without him. Ben is needed elsewhere. Just like Reynolds telling Alt!Ben the history club is for his own ego and that he needed elsewhere.
Then fast forward to Ben in the teachers' lounge with Artz. Ben is complaining about how Reynolds doesn't get what the public school system is about; "Taking care of the kids. That's what is important."
In the next table, Locke says, "Maybe you should be the principal."
"So says the substitute," snaps Artz. (Oh, that's real subtle, writers.)
Locke goes on how Ben sounds like he cares about this place, "And if the man in charge doesn't, maybe it's time for a change."
Ben responds, "Who is going to listen to me?"
Locke raises his hand. "I'm listening."
Now if we represent the school as The Island, then Ben complaining about Reynolds can be seen as how Jacob uses everyone as pawns. And that the real point of the Island is to take care of everyone and the Island, itself. Which only works, again, if Ben has been under Jacob's influence all this time.
Then fast forward to Not!Locke telling real world Ben that he wants Ben to in charge of the Island once he is gone.
BEN: Me?
NOT!LOCKE: I can't think of a better man for the job.
So, like the teacher's lounge, Not!Locke is tempting Ben to turn away from Jacob with the offer of power. Not to mention that Not!Locke freeing a shackled Ben can be seen as being symbolic of Ben being chained to Jacob, that is, without a free will, only then to released. And now Ben has a choice and he chose Jacob.
Think about it, Not!Locke offered him power and Ben still chose to be on Jacob's side.
Why? Because he's Jacob's man.