Primary and Secondary Protocols

The Widmore/Keamy/Dorrit/Faraday Primary Protocol appears to have been:

Naomi lands on the Island safely and makes contact with Widmore's on-Island allies. "Finding Desmond" is her "cover story", but her real mission is to locate Ben.

Daniel and Charlotte's Primary Objective is to secure The Tempest and to disable its Island-wide death-spreading capability. It appears to me that Daniel has taken "Manual Control" of The Tempest at this time, which actually keeps it "in play".
Daniel's Secondary Objective seems to have been the study of the Island's Physical, Temporal and Electro-magnetic properties, possibly to re-enable communications with the mainland. His Tertiary Objective may have been an effort to correct his "memory problem". Having helped Desmond find his Constant (and thus possibly establishing his own) he may have achieved this objective. Note that Daniel (but not Charlotte) was aware (how?) of Keamy's Secondary Protocol.

Miles' Primary Objective seems to have been to locate Ben, using any means available, including telepathy. He's happy to try to extort money from Ben (as he did to the Ghost of that drug-dealing grandson) but he didn't "sign up" for mass murder.

Charlotte's Cultural Anthropological training may have come in handy in understanding and befriending the Hostiles and other Others. Having said that, her social skills need sharpening up, IMO.

The Science Team having disabled the Tempest and having located Ben, the Wet Team's Primary Protocol seems to have been to capture Ben, based on the info gathered by the Science Team and to escort him off the Island, leaving its inhabitants alive but under the new leadership of the Widmore Loyalists.

Ben's declaration to Team Locke that after his capture, everyone else on the Island was to be murdered may have been another of his lies (although it was tacitly corroborated by Miles). It seems to me that it was only after the failure of the Primary Protocol that Keamy initiated the Secondary Protocol which included finding Ben at the Orchid, capturing him and "torching" the Island.