Like I said, I don't know if this is just an obvious fact to everyone by now and I'm just late to realize, but here it is anyways. I was just watching "Dead is Dead" from season 5 and re-watching the scene where Ben sees Widmore off the island (after he got banned for having an affair off island). Widmore tells Ben that "if the island wants (Alex) dead, she'll be dead." or something along those lines.
It donned on me that those were the rules Ben was referencing when he told Widmore he had broken them. The Island was supposed to choose whether or not Alex lived, and when Widmore's man Keamy shot Alex, it broke those very simple set of "rules." Widmore chose for the death of Alex, not the island (or Keamy did, but he acted on command from Widmore.) And obviously, that's why Ben tried to kill Penny.
On a side note, I'm sure in season 6 we'll get some kind of closure between Desmond and Widmore. I bet Desmond will finally get his respect now that he saved Penny.
Again that's just what I thought up, I don't know if anybody else had the same thoughts too haha