The writers were themselves lost in how to keep a critical darling of daring story telling sharp and new episode to episode. In various hits and misses (see, Nikki and Paulo), Ben captured the real danger of a mad man against the basically naive and overconfident surviviors.
As an adult, Ben sought power and control because those things were never a part of his childhood. He became so obsessed with changing his depressing, measly little life that he snapped and committed mass homicide in order to become the leader of the Others.
How can a shy, innocent boy turn into a mass murderer? Then why could many viewers be drawn into his character so much to call him their favorite?
Ben was extremely possessive of the objects, information and people around him. You can see a god-like demeanor in his thought processes, much like a Sim City game player has the god-like authority to build or destroy his town and people at will.
Since Ben did not have a great childhood, he wanted the things normal children had like possessions, objects, toys and adventures. So as an adult, those lost events wormed their way into his dark mind. Instead of material toys, he collected people to do his bidding. If he wanted a fertility specialist like Juliet, he would kidnap her. If he needed a spinal surgeon, he would bribe, manipulate and torture people to get cooperation. Everything around him was his to do what he liked . . . that was Ben's world view.
But at the same time, he pledged some sort of alliance with Jacob, the island master. But we don't think Ben ever saw or spoke to Jacob during Ben's leadership of the Others. We believe that he only got the information from Alpert, and took the myth and manipulated the Others to follow him. He controlled the natives by claiming to be the word of Jacob, when in fact, that was probably a lie.
It was only when Ben actually met Jacob with Flocke, that Ben broke down and his anger swelled enough to kill Jacob with a magic knife. As such, it doomed Ben to his own island damnation until out of pity, he was spared his own death.
Whether that single act of kindness which he never had during his life "changed" Ben to really become "one of the good guys" is not absolutely clear, but he did move the side to allow Jack and Hurley to take the position he most coveted - - - island guardian. Since he could never control the one thing he desired his entire life, the island, Ben at some point was at peace. It did not make up for all the bad things he did in his life, but at least now he realized the errors of his ways. Errors that would never be punished, even in the sideways after life.
