I agree with Murp and I've posted this somewhere before. I believe this is the beginning of a downward spiral for Sayid. The captain is not working for Ben. He is either working for Widmore or someone else entirely. A third party that we are not yet aware of.
Sayids actions are going to cause the people on the island to be attacked by the freighties. This will inevitably make him feel guilty which is why he goes to work for Ben. He is trying to ease his guilt by saving as many people as he still can.
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