I agree with this, the foreshadowing to Jacob making his own rules was when him and MIB were playing Senet and MIB told Jacob that he couldnt move the pieces that way, and when he made his own game he could make the rules...
Futhermore when Hurley is talking about Desmond not be able to leave the island Ben says "that was Jacob's way of doing things" So the protector of the island gets to make the rules as he or she seems fit