Been thinking about this since S5 finale, and some others on here have touched on it as well in part, but I'm leaning more and more towards this theory the more I think about it, especially after seeing LA X...
The first thing that hit me when watching The Incident, was some blatant symbolism. I think the show has usually (to me at least) been rather subtle with clues sometimes, but when we first see Jacob with his bright white shirt, and MiB in his pure black one, I thought "huh, they sure want to make sure no one misses that hmm?". Later in that episode, Lapidus mentions that folks who go out of their way to tell you they're the good guys are usually the bad guys.
Since we've seen the "secondary timeline" (which, to go off tangent here a bit I think is a bit of an homage to Earth X (http://en.wikipedia.org/wiki/Earth_X) we've seen some of the results (in theory) of what the bomb changing things might mean, extrapolating some of these I think shows who's on what side, and I don't quite think it's as cut and dry as "good and evil".
I'm going on the assumption that the Underwater Island we saw was caused by the bomb, and that therefore the Island sank '77ish. This still fits with the Statue being destroyed (Ben mentioned to Sun 'it was like that when I got here', which was '73), and DHARMAville being built. If this *is* the case, then...for obvious reasons...The Swan was never built, meaning no computer, meaning no Kelvin or Radzinski or Desmond to push the button "to save the world". Now I realize that if there's no 'build up of electromagnetic energy' (because it's no longer there), there may not be a need to 'save the world', but (from what we've been told/shown so far) the Swan was designed (post incident) to bleed off the build up slowly every 108 minutes so that a massive release of energy would not cause a "goal catastrophe".
The ship at the beginning of "The Incident" is supposedly being brought there by Jacob (in a manner we're not sure of yet), and MiB seems very against this. Jacob also interacted with a number of the 'core' 815 survivors (many of whom were also on Ajira 316 to come back, including Hurley who Jacob didn't meet till *after* the original 815 crash). Is this indicative of what MiB meant when he said it's always the same? Can we assume as well that Jacob also managed to bring the DI to the Island? Perhaps MiB wants to prevent people from coming to the island to keep such events (the failsafe, the bomb) from happening in the first place? It could be that Jacob and MiB represent not good and evil but "Chaos" and "Natural Order" where Jacob has been trying to make certain events occur, and MiB is attempting to protect the natural "destiny" of things. It could also, in a rather Yin-Yang sort of way, explain why MiB can't kill Jacob directly as there could be a cosmic "need" for the dichotomy.