That's not work. That's a...that's a joke. Rats, in a maze. With no cheese. -John Locke

At the beginning of the season 2 episode, "?," Mr. Eko has a dream in which his brother Yemi tells him he has to find the question mark on the Island, and that John Locke has to help him. Later in the episode, Yemi appears again, this time in Locke's dream, and points the way to the question mark. We know now that the Man In Black appeared to Eko as Yemi and killed him. It appears to me now that the Man In Black wanted John Locke to find the Pearl and lose his faith in the button. Why? The Swan is still a mystery to us. I don't know whether Jacob or MIB knew or cared about the hatch, and given the fact that Kelvin waited at least ten years for his replacement, untouched by the Purge, the Others probably didn't know about it either. Given that life on the Island pretty much continued normally after the Swan implosion, there was nothing permanent or imminent about the potential danger of not pushing the button. It's likely that the DI could have not built the Swan, but then they would have lost out on either or both of the following: the use of the near-endless supply of energy at the site and the opportunity to do some really creepy social science experiments. Locke believed for a long time that it was his fate, first to get into the hatch, and then to push the button. It was MIB who used Eko to cause Locke to lose his faith and ultimately destroy the Swan. Was MIB only interested in sending John Locke along the spiritual path that would end in his death, or did it also benefit him that the Swan was destroyed? Remember those times when Locke did something crazy and you just had to say, "Locke, what the frak are you thinking?" Like when he stopped pushing the button and the Swan was destroyed, and when he entered 77 and blew up the Flame, or when he blew up the Dharma sub, or when Ben blew up the chamber at the Orchid because Locke told him it had to be done. MIB used Locke on numerous occasions to destroy the infrastructure of the Dharma Initiative, whose people had been wiped out to a man 12 years earlier. I think that Jacob and the Others were not just holding MIB prisoner; he was a slave, a sentient creature enslaved as a security system, to check out new arrivals, issue judgments on who is good and who is bad, and protect the Island and its secrets. Remember when Ben used the MIB as a weapon against Keamy's men? Slavery, plain and simple. Add to that kidnapping, lying, murder, and you have Jacob, or at least the people who act in his name. And now Jacob is dead, and MIB is free. And, boy, is he mad! He's recruited Claire and Sayid, and possibly Sawyer and Jin, and he's now wiped out a large number of Jacob's people at the temple. This was without a doubt the best Smoke Monster scene ever.
The point is that the balance of power has shifted, the tables are turned, and MIB is the one who has followers now, while Jacob is mere ash. If MIB's people lie, and cheat, and manipulate, and commit murder in his name, what makes him any worse than Jacob? Maybe MIB and Jacob are not the black stone and the white stone, but longtime rivals, both of them morally gray, who lure people to the Island, and, like flies to wanton boys, use them as pawns, like Locke's mousetrap game, or that Skinner box, the Swan.