What about this idea:
The Island represents the Garden of Eden; a place that has mystical powers, such as healing and allowing people to never age. Repeatedly, Jacob (God) gets people to come to the Island, which would represent mankind being created in the Garden. Yet, as the other guy says (Satan), whenever this happens, those people just end up quarreling and destroying each other (representing Adam and Eve's sinful nature and corresponding banishment from the Garden).
The other guy besides Jacob, who would represent the Devil, would greatly like to kill God, but he is not capable of doing so. But like in the Garden, the Devil changes forms in order to manipulate people (like Eve). Ultimately, he is able to manipulate Ben into killing Jacob. This could in turn represent the crucifixion of Christ, as the Devil has manipulated mankind (Ben) into killing his own creator (Jacob, who brought him to the Island).
Lots of loopholes in that theory, but it's a start. It also doesn't quite explain all the Egyptian influence.