I don't think Sayid acted upon some moral judgment of Michael's killings or of his spying for Ben. Possible that he was trying to get a better view of the bigger picture by seeing what happens if he forces Michael face the Freighter people. He might have a plan we're not aware of yet- mind you, he was a torturer so power games based on psychological manipulation is one of his tricks that might come handy in times like this.

In any case, I wasn't too happy to see him go tell on Michael though.

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"Bear...? Is that you?"-- Hurley S03E4