Yeah I think that's how Sayid begins working for Ben because outing Micheal. Cause Sayid beleives what the captain told them but once he realize he screw up he working for Ben. Don't think Ben knew that Sayid was going to be going to the Freighter.
Gonna be a long month to wait to see what happens next, but this episode did answer some questions.

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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