I'm not sure Jacob is good, but he certainly believes he is good. His mother told him, and since he loved her more than anything and wanted her approval (he didn't even despise her for killing his real mom) he grew to believe that he was in fact protecting the island. He killed his brother by impulse, that doesn't really make him evil. Neither does his brother killing the crazy lady, it was clear that he was sorry afterwords.
I don't think that MIB is no longer Jacob's brother. In the discussiions he had with Jacob AFTER becoming Smokey he expressed the same contempt for people he did back when he was in the village and the same desire to leave. Smokey/Jacob's Brother/Locke has been very sincere (crazy mother, he wants to go home, the island doesn't need protecting) as to the ends, just not about the means (killing the candidates). I know I would kill the candidates if they told me I couldn't leave for no apparent reason.
Why wouldn't MIB's mother let him leave? I think it's because he really wanted him and not Jacob to become the new protector, and she was blinded by this. Letting MIB leave would not have been a problem, since a)there was Jacob to fill up the "sucker" position and b)Smokey wasn't unleashed. Was his mother afraid that MIB would return to the island with other people to get the light??? NEWSFLASH: Jacob is the one constantly bringing people to the island. And we saw what happens when you go into the light, so rationally speaking, why would the island need protecting??? Now I know that Egyptians believed that if they don't follow certain rituals every morning the sun won't come up (lol), but apart from that, protect it from what?