What I am presenting here is merely a theory on the rules. This is only speculation. Maybe we can come up with a more complete list rules as we theorize about this together.
What have we seen so far…
An Other has never killed anyone directly that was on ‘the List.’ ‘An Other’ has only killed ‘An Other’ and not suffered punishment after consent was given (i.e. Klugh* told Mikhail to kill her.) When Juliet killed Picket, she was banished and marked.
Ben has never killed anyone on the list. However, he put Goodwin in a situation that would lead to his death. In a sense, island justice was allowed to play out, so Ben’s hands were stain free. Ben still lives by the rules as we see with the freighter and his not wanting to kill innocents.
1. Everyone on the List are considered the good guys and are safe from harm.
2. The others have never killed anyone on the list.
3. The others only kill one of their own after consent has been given.
4. Those on the list are to join and be accepted by the others.
5. Punishment for the death of an other by an other means banishment and marking.
6. Those on the list can be put into harmful situations that may result in their death.
This must mean that Alex was on the list. Ben never expected her to be killed in that situation. In this case, the rules were changed because someone on the list was murdered by one seeking communion with the island. It was not supposed to happen.
Ben specifically said that Widmore had changed the rules, not that he didn’t abide by the rules. By allowing Alex to be murdered, Widmore shows that he has power over the rules. The rules are there to protect the innocent. By murdering Alex, Widmore is now no longer able to protect those on his list. Hence, the introduction of Sayid as assassin. Sayid is now going after all of those that were on Widmore’s list. Now, Widmore is no longer able to protect them because he changed the rules.
*thanx to KoozyK for the correction.