When you lie down with dogs, you wake up with fleas. Khan freely joined forces with our enemies and, as an apparent US citizen (very different from Awlaki), abdicated his rights to a trial of his peers when he sought to kill Americans or destroy the country of his birth.
The rules of warfare are very clear and have not changed considerably during the past 100 years or better. Khan aligned himself with our enemy with whom we are at war. That made him an enemy combatant who becomes a legitimate target. Under these circumstances, he's not entitled to the "niceties" of arrest and trial.
This was a much cleaner and a more politically expedient for this administration. If they had captured Awlaki. Where would they have kept him? Gitmo? When Obama said we should close it down.
Can you imagine the political implications of what Obama would have to deal with if they had of captured this guy.
Basically I am trying to (other posts) state that if Bush had done this the Left would be calling for impeachment. Because there are some “conflicts” with the Constitution that are obvious.