Certainly covert actions would be viewed as illegitimate by those they are employed against. This is a risky business, but Slap raises a good point, and added the qualifier of "plausible deniability." Of course these things can blow up in one's face. Take our actions to put the Shah in power in Iran. The Iranian people will not soon forget or forgive that bit of Cold War manipulation.

What we seem to discount, however, is that legal, totally overt actions can be equally or even more damaging to our security. Again, with Iran as an example, how do we think the Iranian people perceive the US in our hard, overt sanctions against Iran intended to deter them from developing a nuclear weapon? Even Iranians who do not believe their nation needs such weapons tend to believe even more fervently that the US has no right to curtail Iranian sovereignty to be something less than the sovereignty of those nations currently in possession of nukes.

We, being a nation of laws, tend to put too much faith in actions being ok so long as they are legal. Nothing could be further from the truth. The primary test must be one of perceived appropriateness, not legality. Often this is primarily a constraint on "how" rather than "what" one believes they need to do. The vast majority of our actions in response to the attacks of 9/11 have been legal. But the majority of our actions have also been perceived as inappropriate by those they affect and by many who watch from afar. It is the inappropriateness of our responses that is, IMO, the primary reason that for all of our tactical successes we are failing at the strategic level.

Too often we are unwilling to compromise tactical gains (that are objective, measured and reported to measure our success) in the name of attaining greater strategic gains (that are subjective, nearly impossible to measure, and therefore largely discounted in importance). How many times has President Karzai asked for reasonable constraints on tactical operations in his own country to be told "no" by the same American government that professes to be there as a guest of a sovereign nation with the mission of enhancing the legitimacy of their government? We say one thing, but then our actions have the opposite effect. We even publicly chastise President Karzai as being ungrateful when he dares to stand up for extremely reasonable sovereign rights that we would certainly demand if roles were reversed.

So our occupation of Afghanistan is both physical and by policy. And the resistance insurgency there is very strong as a result. This resistance insurgency will wane rapidly once we back off on both of those lines of provocation. (However the revolutionary insurgency against the government we elevated into power will continue regardless of what we do, we need to accept that fact as well).