I've thought for a while now that Ben was never following orders from Jacob. It has been MIB the whole time. But he's been using Jacob's name to get Ben to put all his faith in Jacob (the name) so that when he meets the real Jacob with the Locke-alike he will realize that Jacob (the real Jacob who Ben thought he was following all along) doesn't care about him. Which will make it easier for the Locke-alike to convince him to kill Jacob. Too many Jacobs in that post haha.
But Griz, Ben was never given orders directly from Jacob they were always through Richard

JACOB: You like it? I did it myself. It takes a very long time when you're making the thread, but, uh... I suppose that's the point, isn't it?
LOCKE: Hello, Jacob.
JACOB: Well, you found your loophole.
LOCKE: Indeed I did. And you have no idea what I've gone through to be here.
BEN: Have you met before?
LOCKE: In a manner of speaking. [Whispers] Do what I asked you to, Ben.
JACOB: Benjamin... whatever he's told you, I want you to understand one thing. You have a choice.
BEN: What "choice"?
JACOB: You can do what he asked, or you can go, leave us to discuss our... issues.
BEN: Oh... so now, after all this time, you've decided to stop ignoring me. Thirty-five years I lived on this island, and all I ever heard was your name over and over. Richard would bring me your instructions--all those slips of paper, all those lists--and I never questioned anything. I did as I was told. But when I dared to ask to see you myself, I was told, "You have to wait. You have to be patient." But when he asked to see you? He gets marched straight up here as if was Moses. So... why him? Hmm? What was it that was so wrong with me? What about me?!
JACOB: What about you?
BEN: [Whispers] Oh. [Normal voice] Well...
[grunts]
[pants]
JACOB: [Gagging] they're coming.
LOCKE: What?
[Jacob gags.]
LOCKE: I can't hear you.
JACOB: They're coming.
I do ponder over this fact that it was MN2 that was asking forhelp. If Jacob was free to roam about well and he does admit in this scene that MN2 found his loop hole well. And if there is a need for a leader well what does this mean for the poerws of Jacob and MN2