Chomsky's counterposing of rights against legitimacy, his raising of "bad" state actions, and his bemoaning of a lack of "inherent legitimacy" indicate that he thinks legitimacy is a merely neutral moral and legal (nonpolitical) category that can be separated from the state, a good unit of measure that can be rehabilitated. He doesn't think that things like rights, legitimacy, crime, genocide, etc. are creations of the state and essential to its maintenance; they are not just the bases of it. Which is to make the point many have made about him: He's an anarchist whose problem with the state is its moral compass, not its structural brutality.