I don't think the MIB is the bad guy, I think he was just a surrogate of the Smoke Monster like Locke is now. I think the Smoke Monster is the true "bad guy" though I'm not really sure anyone is truly the bad guy on the show. We have Jack/Locke, Ben/Widmore, and other people who have caused factions and divisiveness, and now we just have another similar dichotomy between Jacob and The Smoke Monster.
the man we saw with Jacob is sort of a red herring in a way.
makes one wonder if the body Jacob uses in the show is actually Jacob himself, or just a surrogate body as well. I actually lean towards it -being- Jacob, though perhaps not his true form. Since he has so much faith in humanity, he chose a human form. Whereas The Smoke Monster is less believing in humanity, and just wants to go home.
I am now thinking that the clanking sounds it makes when it moves around are the sounds of chains. I think Jacob controlled it, and used it as a security system keeping it secure in The Cabin. I think in a sense that Jacob did some wrong things for the right reasons. And we'll see the consequences of that play out as we learn more about The Smoke Monster.
In time we may not be nearly as sympathetic to Jacob as we've been. We'll come to see him as a flawed good being just like Locke or Jack.
Vice Versa, we'll be more sympathetic towards The Smoke Monster, who while he may do bad things, is simply a prisoner trying to get home.