I don't think Ben and Widmore ever had rules, they just thought they did. All along it was only MIB and Jacob playing by rules - Widmore/Ben were mere pawns and Ben has realized this, so he shot Chuck b/c he knew it's all going to end now.
Also, I think Flocke will remain as Jack's nemesis at the end. After shuffling all the episodes you can really see how those characters interactions have contrasted Jacob/MIB, even by the way Jack has beat up Locke in the past similar to Jacob beating MIB so many times. Of course there hasn't been as much airtime for Jacob/MIB, but I now realize the show has been leading to Jack and (F)Locke as the potential remaining inhibitants.
That said, I have no idea what Desmond is up to...and how Hurley recognized Ana Lucia in the FS, so there's a chance I'm wrong about everything! haha.