I've always been in the Jacob = good camp as long as we've been debating good vs. bad. But, and I'm sorry I don't remember who first brought it up, someone mentioned the old computer game Myst. I played it years ago and I don't remember it all, but basically, you puzzle your way through this mysterious island where you are given clues by these two brothers who are each trying to convince you to help them because they are the good guy and you should not listen to the other. Long story short, at the end, if you choose to help either of them escape, you lose and end up trapped yourself because the real good guy that needs to be saved in the game is their father.
So, while I'll never buy that MIB is good unless they cram it down my throat on finale night, I will admit that I wouldn't feel comfortable with Jacob as my best friend either. I'd settle for having Widmore come to the rescue and shut down the whole operation, trapping both MIB and whatever is left of Jacob. I could buy that. And maybe Widmore's ties to the island go back further than we have been shown.
I always had a problem with his line, "The island is mine, Ben, always has been". Could it be the young man we met in the 50's wasn't the first time Charles had been there? Maybe 'Charles' is his latest persona and he was there to keep both MIB and Jacob in check. Do we know if Jacob was able to leave the island before Ben took over? Did Jacob influence Ben into power to get rid of Charles and gain his own freedom? This would explain why Jacob and MIB both acted as though there was something to worry about when Jacob said "They're coming". There's probably not enough time left to go this far into it, but I thought it was an interesting idea, though.