Let me address the clear parts of the show. We see that Jacob was the master planner in the candidates lives, watching them from birth and guiding them, sometimes with prescience that implies his ability to travel time (or just be around for all of time) that is very subtle but certain. For example, helping James to hold on to his hate. Note later he says how they were all flawed... yes, but couldn't he have helped them to be otherwise through their lives? He might have no responsibility, but what he did instead was start exploiting it.
Jacob's mother was a murderer, and he sides with her. Knowing this he sought to beat his own brother, and put him to a fate worse than death (according to the murdering-mother). While it appears the MiB fails to get off the island, if he too moves on, eventually, his death allows that release. His struggle is another thing, a visious struggle to be free by a caged animal. But Jacob... what of him?
Jacob's rules, we know, are not real rules, I think, because, for example, Kate's name would not be crossed off "just by a line in a cave", but as a result of said rules. There were several references in Across The Sea to just making up the rules, and how eventually Jacob would get to make up his own rules. That is just what we must presume he did. And they were some damned sick rules. We have no reason to think mass murder is needed, in particular, to solve the threats to the source (helping the crash victims escape might do?), and no reason to blame them all on the smoke monster. It would seem that Jacob in one way or another took up his mother's predictions, either by manipulating events so it would happen that way, or perhaps more directly, ordering it through his representatives. Given the shows penchant for, I think, implying perhaps he merely "allowed" these representatives to do these things in his name in the spirit of "free will"... but when a near omnipotent power "allows" things, how is this different from "approval"?
Richard called him on this from day one, why intervene? "So they don't win!" Simple.
Further, for someone to be held to account for their free will they need INFORMATION. The free will to buy this or that tool, to create this or that device is informed only by the situation... one must know more facts of the matter to become more free, and thus more responsible for their decisions, because it becomes more intentional. Jacob's "game where you don't know the rules" is fairly sick, and only really a game for the few that know the rules. Even in Calvinball you have to shout out when you create a new rule.
Ironically, I believe Lost tells us even Jacob doesn't really know any real rules, we see only the made up rules, and the underlying rules, say laws governing the energy, are totally of no interest to Jacob as far as we know him. Of course Lost the show shows a LOT of interest in the specifics... and this is what not only Dharma represents, but also the "intelligent men" MiB refers to. Some people do want to study the light, and they prove there are scientific measurables to it, such as magnetism, and four dimensional timespace gradients, and we see there is a material component to whatever energy we are made of when our body dies (presumeably the energy the light is made of if KillMother was correct), and so we can in this state still, sometimes, interact with the living.
These are all rules of physics we don't know the detail of, just the resulting phenomenon. The rules we see, of candidates, of life-long manipulations and secret trips, notebooks from the future and long cons embedded in longer cons --- these are Jacob's rules. The reason we don't need more detail, is Jacob was willing to change them. A line in a name... hey, the only rule is Jacob makes the rules. Some are complaining about holes in the "real" rules, meaning the "immutible rules", and I myself will enjoy filling in those gaps with many things I feel lost implied without saying explicitly, the fact is the story without holes, with a complete picture, is this one of what the rules were.
You don't need to know what they were in every detail because Jacob didn't write them down (that we saw... perhaps in the tapestry? :), he could return an expelled player, or not. He was winging it too. Those rules did not ultimately create, e.g., the lists people died and killed for. Jacob might just being going, "gee, she's a mother, probably won't ask her"... and "but hey, she's here at the fire with us, what the hell, you're still in kate" and perhaps unspoken, "you're out, but I can't argue with you now so I'll say it's just a line in a cave"...
If there are real rules, the type an obsessive compulsive would make, and he hid them so deeply, then again... Jacob's character is in question.
What I'm saying is... the dark current of the show, the murder, torture, mayhem, brutality... that's Jacob's doing. That's not MiB's. MiB was just a caged monster, like the Minotaur, captured ultimately to play a role in a maze built by a genius commissioned by a mad king.