I'm pretty sure sure US intel knew what the US citizen, Anwar al-Awlaki was doing in Yemen. That "we" didn't know was likely by design.<quoted text>
We have no idea what the citizen in Yemen was up to, the government ordered his execution not his arrest and trial.
The impoverished Yemen looks to it's pipelines and ports for 70% of it's entire economy and for the strategically located nation to remain somewhat stable has required outside help from the likes of Jordan, Qatar, Saudi Arabia and by proxy the US.
Aside from al Qaeda setting up shop along the coast of the Aden Sea, Yemeni tribesmen frequently blow up the pipelines to the Red Sea as a way of protest. That the US doesn't trade with Yemen is irrelevant, someone does and would have to go elsewhere to purchase crude creating uncertainty(higher prices).
Drone warfare changed everything, the superpowers used to send in political sht stirrers and even assassins. Satellite technology in combination with drones seems far more effective particularly considering the psych factor drones place on those being hunted.