This is my take on it.
-Imagine that the island is a maximum security prison.
-The "Prisoners" in this prison is the evil, and if it escape the world would be in danger. Just like in a real prison if a serial killer or mass murderer escape he'd be a danger to society.
-Jacob is the Warden of the prison, he's in charge of the day-to-day operations, making sure the prison runs well, and is effective.
-The MIB/Smokie is the Prison Guard. In charge of actually keeping the security of the prison intact. Making sure no one escapes.
-The Prison/island has rules of conduct, just in the real world a prison has to follow the rules laid out by the government (State or Federal). For example, a Prison Guard can't just kill a Prisoner for no reason, but if the Prisoner tries to escape then he can shoot him. The Island also has it's own rules about killing and escaping and such... Who made these rules and enforces them is still unknown, but probably the source of some of the "ghosts" we've been seeing.
At some point in the far past, Jacob & the MIB took on their roles, Warden & Prison Guard. maybe they chose to do it for a good cause, maybe it was the promise of eternal life, maybe they were tricked in to it. How ever it happened, they took their roles. Maybe they were both good guys back then. Or both just normal people, neither super good or super evil.
But over time the MIB began to get tired of his role as security guard. he was stuck in this prison 24/7 pretty much just like any of the actual prisoners were. he became resentful and angry. Why should he care what happens if the "prisoners" escape? he has nothing to do with the outside world anyways and besides everyone who he ever meets (people that come to the island) always end up the same, fighting, killing, etc... Why should he spend his life protecting people like that?
Jacob, on the other hand, never lost sight of the goal and what they were doing there on the island/prison. By bringing people to the Island he is trying to show Smokie/The MIB, that not all people are evil, that some are good and just and that the jobs they (Jacob & The MIB) are preforming are of great importance.
But it's too late now. the MIB is determined to "quit his job" and leave the Island. If he does so, then there will be no guard there to stop the "Prisoners" from escaping. And they will escape and evil will take over the earth. But the MIB no longer cares, as far as he is concerned the people of the earth are already evil and corrupt.
The first thing the MIB had to do was get rid of the "Prison Warden" before he could quit/leave. Now that he is done that, all that is left for him to do it make his own "escape" from the "prison" and the rest of the world be damned.
So I don't think the MIB started out evil, but he has become selfish, caring only about himself, and he is willing to damn the rest of the world to get his way. So now, he is for all intents and purposes, evil. Because what he wants to do for himself will cause evil to be released upon the world. So he has to be stopped.
Or... Someone will have to take over his role as "Prison Guard", just like someone has to take over Jacob's role as "Warden".
I'm betting Jack becomes the Warden and Sawyer becomes the Prison Guard. Stuck together on the Island for eternity. Well, at least until history ends up repeating itself, 1000 or so years from now when Sawyer tires of his job and tries to kill off Jack and escape.