I know I just posted a theory on the Losties involvement in the incident, but my mind had been on LOST all day.
I think the true "bad guy" of LOST is Mother and I'll give my reasons why.
Mother, firstly, kills Jacob and the MiB's mother and steals them as her own. She raises them as her own, lies about where they come from and puts the idea in their heads that they can't leave. I think it's fairly obvious Mother did this to ensure herself someone to follow as the next protector as soon as she thanks the MiB for killing her. She took children because they were easy to manipulate into believing that they HAD to do it and HAD to stay on the Island and she knew, no matter what, one of these kids would end up being the next in line once she died.
Jacob was naive as a young man up until sometime after he created the smoke monster. The entire time we see Jacob in "Across the Sea" he comes off as really hotheaded. The Man in Black was right all along, in that they didn't HAVE to be there or be the protector, Mother just lied to them about that to ensure she had someone to follow her. Jacob, being naive, doesn't truly believe MiB and sticks with the only person who took care of him in his life up to that point, Mother.
It's ironic because MiB could have left the island at any time and it wouldn't have mattered, unlike what Mother told him when he decided to join his real people. It wasn't until Jacob himself turned his brother into the Smoke Monster that he really, honestly and physically could NOT leave the island under any circumstances.
It isn't until years and years on the Island that Jacob starts to see the error of his, and Mothers, ways. He realizes she was wrong and that all people aren't bad like she thought. He realizes that he can leave it up to others to make their decisions (i.e. the candidate) and he didn't have to kidnap anyones child in order to have someone be the next protector. I also believe this is why he crosses mothers off his list, as he doesn't want to split mother and child up as he had been when he was split from his real mother.
As for proving MiB wrong about human nature, I think Jacob does this when Jack chooses, willingly, to be the next protector of the source. It proves that there are people who just genuinely care about something, and they're not all out to get each other like Mother and MiB think. It's so interesting to see how in such a small amount of time on screen (but a LONG time in the story), we see Jacob go from a naive guy who will do anything his fake Mother tells him to do to learning from the mistakes he made and trying to right his wrong.
EDIT: THOUGHTS ON THE SMOKE MONSTER: In writing this another thought came to me. I believe the Smoke Monster was only created because Jjacob was made so he couldn't kill MiB by mother, so when Jacob threw his brother into the Source, it killed his physical form, but because he couldn't kill him the source had a discharge of sorts and that was the Smoke Monster. Kind of like the Source and the Protectors abilities not meshing and spitting out the monster.