As far as Saddam's authority being legitimate, we actively supported Saddam in his early years in power, and recognized him as the legitimate leader of Iraq. Granted, the mistreatment of his own people would suggest that he has given up any rightful claim to a position of authority, but I do think that it is ultimately up to the people of Iraq to rise up against him--much like our nation's founders rose up against King George.
When we start getting into the area of questioning government authority, we cannot avoid wondering whether or not the government of the United States is legitimate. Sure, it was lawfully established under the Articles of Confederation and refined by the Constitution, but we can see throughout history that our government has moved further and further away from its intended role. The Constitution no longer has any meaning to those who govern.
I think a much bigger issue we need to address is determining the legitimacy of our own government. Can a government wage a "just war" against another nation while ignoring the more immediate threats it poses to its own citizens (e.g., over-regulation, over-taxation)?
I'm not saying that we should take up arms against the government. I'm merely pointing out that our government is hardly a "moral authority."