Two Possible Scenarios

There are two possible scenarios regarding Jacob and his adversary Dark:

1. There is a centuries old cycle between two men that never seems to end. One wants to end it now, by killing the other, although it appears he can't be the killer himself. There is no real good or evil struggle here. But the cycle can also end if fighting and corruption by visitors stop. Jacob keeps bringing visitors to the island, hoping that will occur, although it hasn't yet.
2. There is a centuries old cycle between Jacob / free will / virtue / redemption vs. Dark / violence / corruption / destiny. We remember that the principle, unique human characteristic of free will separates us from being violent animals. Dark actively abets the violence. Jacob, being a believer in free will, can not help the visitors in any way or he will break his own faith.
   

There are still some reasons to believe both are valid theories. I tend to side with Theory 2 and explain Jacob's maltreatment of Sayid as a necessary corollary of developing a righteous sword for the good guys (e.g., Jesus needed a Judas). For a more detailed look at why I believe that, read this post regarding Jacob and Dark | The Struggle.

Either way, it appears that Dark has finally won by finding a loophole to kill Jacob. That is, until Jack and his group break WHH and blow up the Swan, which gives Jacob a new chance at life, as well as for each of them.