I don't think successfully throwing out a colonial regime earns you legitimacy. In the initial phase of the fight it will earn you an allegiance in a "the enemy of my enemy is my friend" sort of way, but that is a far cry from legitimacy, as the events after the fall of the colonial regime often prove. Once the common enemy is gone then the true beliefs and their associated loyalties and legitimacy show themselves. By then, it is often too late.
What it can earn you is respect: the kind of respect born out of fear. That can be turned into power, but it is still not legitimacy. We had the power after the fall of Saddam but we were not going to use it as some others (i.e. Ho) would to consolidate their governments. As you say, no government (even, or perhaps especially, the U.S.) garners legitimacy from 100% of its population. Of course, it is easier to up your legitimacy numbers if you simply kill off those people who don't see you as legitimate - a method you are unlikely to see in the new, updated 5-34.
This just goes to prove that efficiency does not create legitimacy, despite what some of our current COIN ideas tend to espouse.
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