Maybe Libby once was on the island before the plane crash and she can't die and that's how she began working with Widmore. Or maybe Widmore has some way of knowing Micheal is on the boat working for Ben and has some kind of ghostly way of using Libby to try not to get Micheal to do what Ben wants.
I kind of like how Ben said to Micheal that they didn't tell him to kill anybody but just to set Ben free and understanding how he might of reacted because they were holding Walt.

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Standing in the ocean with the sun burning low in the west
Like a fire in the cavernous darkness at the heart of the beast
With my beliefs and possessions, stopped at the frontier in my chest
At the edge of my country, my back to the sea, looking east