I don't think the point of the show is who's bad and who's good, it's not as black and white as the rocks make it out to be anyways. Jacob and the Man In Black are fallible, and Jacob has lied in the past. It's less that Jacob's good and more that Jacob's the lesser evil- but I digress. It's not about that, not really. It's about the choices the characters make, it always has been.
Jacob said tonight, that on the island the past doesn't matter. But it does, the whole show has been built around these flashbacks and seeing how the actions and choices and things that happened in the past affect the cast while they're on the island. We get to see these people change- look at Ben, look at Richard, Jack, Sayid. Sawyer. The inevitable final confrontation isn't going to be bad vs. good, it's going to be friends against friends.
And holy shit did we get some answers tonight, btw. xD