The rules were yet another thing that were never properly covered in the show:
- what exactly were "the rules"?
- where there a different set of "rules" for Ben and Widmore as there were for Sam and Jacob?
- who established the rules for Sam and Jacob - were these physical limitations/restrictions assigned by some omnipotent entity? or were these rules an agreement that they had with each other?
- if the rules were an agreement, then surely a "bad" guy could violate such rules
- if the rules were fixed, then why would young Jacob need to taunt Sean about not being able to kill Sawyer?
One of the the neat ideas that they came up with that they never properly developed, IMO.