Ben, along with the audience, has been led to believe that despite his loyal services to the island, he had lost favor with Jacob, who never cared for him.
Ben's assumption made sense to the audience, because most of us believed at that point that Ben was holding Jacob prisoner in the Cabin. We were also lead to believe that Jacob's new chosen one is John Locke. We, just like Ben, were wrong on both counts. It still seemed as if Jacob had disowned Ben, when he told him the infamous line that lead to the stabbing- "What about you?"
However, While watching Jacob's interaction with Ben in "The Incident", I realized that couldn't be further from the truth. Notice how respectful Jacob is of Ben during the whole conversation. Asking him if he likes the tapesry, reminding him that he has a choice. He even listened to Ben's entire rant with tears in his eyes, because he is genuinely sorry for hurting him, and knowing he has to do it once more to get Ben to do what needs to be done.
That's right. I'm completely, 100 % certain that Jacob planned to be killed. I do believe that he'll come back in some fashion, but that's irelevant at the moment. He knew that he had to die, as his death is probably a part of a counteractive plan to X's "loophole" plan. I believe that Jacob knew ahead of time of X's plan, and had much more time to plan one of his own. And the most intgeral part of that plan is his most devoted follower, Benjamin Linus.
I believe that Jacob wanted his death to be by Ben's hands, in order to "Sharpen" him. Why? Because I believe whatever Ben went through in The Temple had changed him forever. Benjamin Linus is and always has been Jacob's ultimate weapon against X. And I believe that process enabled him as the only one that can kill X, and rid the island of him forever.
So, given all that, let's examine the circumstances of Ben's downfall, that made him think he had lost favor.
It all started with the tumor on his spine. That's when Ben started thinking that for all of his sacrifaces, Jacob had forsaken him. But notice what happened merely two days after Ben found out he had a tumor? "A spinal surgeon fell right out of the sky." Jacob brought Jack to the island, in order to save Ben's life. So then, who had given him the tumor? X. Parlty because I believe that while Jacob's abillities are associated with healing, and X's with death, but more importantly, both because it made Ben lose faith in Jacob, and because X wanted Ben Gone.
Next off, we have John Locke's arrival to the island, seemingly as Jacob's new "Chosen One." However, we now know that was never the case. While I believe that Locke was important in the grand scheme of things, Jacob never meant for him to lead The Others. Frankly, we have no evidence that suggests Jacob was unhappy with Ben's leadership, or that any of The Others were. That is, until Ben started thinking he had lost favor.
Then we have the arrival of The Freighter, and the seeming end of Ben's leadership. Now, I personally believe that Widmore is working for X. Widmore wants the island all for himself, and X probably promised him as much once everyone else is gone. Killing everyone on the island certainly seems to fit with X's plans, and Alex's death benefitted him in manipulating Ben against Jacob. Ben was then forced to move the island, and busied himself with revenge against Widmore's people, who were X's off island people IMO. Then Ben found a way back to the island with Locke's death, and the rest is history.
I don't know for sure if X knew that Jacob planned to use Ben against him. However, I think that his use of Ben in the loophole plan is mostly an afterthought. The tumor, and The Freighter indicate that he wanted Ben gone, but was perfectly willing to use him if he had to. If Cabin Christian is working for X, and wasn't completely lying to Locke, then X meant for Locke to turn the frozen donkey wheel. That makes it Ben's part seem irrelevant, as he simply wanted Locke off the island, in order to be killed. However, Because Ben believed that he had lost favor, he improvised. And seemingly thankfully for X, things did work out in his favor. Therefore, I think he didn't really think to use Ben until he saw him on the Hydra Island.
What makes me so sure that X wants Ben gone?
Well, it's mostly two things. The first is that two of the apparitions associated with X seem to detest him.
Christian: And since when did listening to him get you anywhere near worth a damn?
Falex: Listen to me, you bastard! I know that you're already planning to kill John again. . Listen to me, you bastard! I know that you're already planning to kill John again, and I want you to know that if you so much as touch him, I will hunt you down and destroy you. You will listen to every word John Locke says, and you will follow his every order. Do you understand?
Interestingly, both apparitions favour Locke. Christian saying he believes in him, and Falex warning Ben not to harm him.
The second thing is the fact that when the Others had Jack, Kate and Sawyer, X tried to manipulate Locke into "Saving them." But what he really wanted Locke to do was to grab Jack before he could do the surgery. X wanted Ben to die.
Anyway, that's my two cents.