I don't think that DHARMA is the top of the organization but I do think that all of these mentioned above are connected. It's all some huge conspiracy and the DHARMA we know from the island was just one of the branches. I think that no one is free from this and every action that is taken to oppose any part of the group is countered with tighter control. The purge that Ben took against the DHARMA inhabitants was possibly just a test. He felt he was taking control while really he was just being given a set of instructions to see how easily he minds. I think that he does try throughout his life to counter these folks but I'm not sure how much of what he does is actually serving them. As clued in as Ben is, the conspiracy goes far beyond any one individual.