I don't think MiB and Jacob are the same entity, but are tied together in some destined way. MiB doesn't like the arrangement and wants to change it (gain his freedom).
I think what "Damon" was hinting at is actually more appropriate in the sense that any being is capable of actions that could be deemed "good" or "not good" (evil?), "chaos" or "order."
What it comes down to is what a person's extremes and averages are. You can observe someone who lies all the time, but never kills anyone. Maybe they're leaning on the "evil" side of things, but they aren't by nature a flat-out "evil." You can observe someone who can be nice to people but then occasionally kills someone out of the pretense of protecting their agenda (not out of self-defense). That person is "evil" by nature.
Benjamin Linus is an example of evil. If you think only of his love for his daughter and the other good things he has done, you might disagree. But remember... he not only brutally tortured people, he directed others to kill people. MANY people. I'm sorry, but just because a person is "outside" your agenda, you don't kill them.
Sayid Jarrah is an example of evil. Yes, he has done plenty to help others. He has shown the capability of love. He has professed that if he could have avoided his killer ways, he would gladly do so. But he didn't and cannot. It is in his nature to kill for hire, and has done so. When you observe all of those scenes where he murdered someone, was it self-defense? Was the person that he was eliminating one who had committed murderous crimes, and Sayid was the "judge/jury/executioner"? No...
Is Jacob good? It appears that he is... although he has allowed people to die through indirect actions of his own, he seems to have done plenty of deeds that could be considered good.
MiB is the other entity that Jacob must "dance with" through the course of his existence. For some reason that we've yet to know and understand. Hopefully soon.
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