I kind of get the feeling that all of the freighter people are in cahoots to test Desmond and Sayid. I think they knew all along that Michael was the spy and they were just letting him think they didn't know until they could figure out how to use him to their advantage. I don't think the Captain seemed at all surprised by what Sayid told him about Michael. He actually looked a little pleased...like he was hoping all along that Sayid and Desmond would prove themselves to hate Ben as much as they do. It was more important for them to find out where Sayid and Desmonds loyalties were than it was to find out that Michael was Ben's spy.