Check out Totally Lost at EW. They are going through the same stuff that I have with friends and in previous posts. To be absolutely clear, the suggestion that Jacob is a God, Greek, Egyptian or otherwise, is not to suggest that he is a good guy. His social science experiments would get rejected by any decent research ethics board. And Flocke is not a good guy either. Faith vs. reason, fate vs free will are (to be all obscure about it) orthogonal to good vs evil. That is, they are different dimensions. Just as in dungeons and dragons one can be evil and lawful or good and anarchic (I forget what it is called in the game), one can believe in free will and be either good or evil.
How we interpret some one's good acts depends perhaps in part on whether we think someone has free will or not, but the acts themselves or the goals themselves (depending on what we are focused on) may be viewed as good or evil. I am not a philosopher so I could be very wrong here.
While some many ponder Jacob's goodness by denying his responsibility for Ben's acts on his behalf (because he might been listening to Smokey all along), the experiment of free will versus fate cannot justify Jacob's casual use of people (Black Rock passengers, for instance). Only if the game of free will vs. fate is necessary to win the larger game of keeping Smokey bottled up is Jacob's game playing justified.
It could be that there is a utilitarian logic here about the greater good.
Maybe we will eventually find out. Maybe not.