I think this is pretty in character for Sayid. He's a moral guy, and as far as he's concerned, Michael shot two of the Losties by making a deal with the original enemy...Ben. Sayid is good at honoring allegiances, and with Michael, he bailed on everyone else but his son. Now that he's partnered with Ben, Sayid's departure from the island to the freighter was for the benefit for every Lostie.

Seems like a conflict of motives between the two, but we know better. If Sayid needs to use Michael as a pawn to ruin Ben's plans to hopefully benefit Sayid and his friends, he will do that.

Albeit, it may not play out very well, but Sayid's intentions I think are honorable to those left behind.