Look at the options more carefully:
(1) Leave al-Awlaki alone, situated in the middle of AQAP home territory, and hope that he doesn't succeed in his evident ambitions to coordinate attacks against Europe, America, India, Russia, and Indonesia. This is the strategy Clinton employed against Osama bin Laden and Ayman al-Zawahiri. You and I might debate it, but a realistic analysis of the circumstances of al-Awlaki has to acknowledge that the strategy was discredited. Consider carefully what the real differences between al-Awlaki and al-Zawahiri actually were.
(2) Kill al-Awlaki with an air strike. Here, we have the benefit of seeing the result of this strategy, since it's the option the US actually took. Result: 14 people dead: al-Zawahiri, his son, the editor of al Qaeda's English-language magazine, the day-to-day operational leader of AQAP, and 10 other people. Assume only al-Zawahiri, the editor, and al-Banna were actually meaningfully hostile to the US: that's a death toll of 11 innocent people.
(3) Invade Yemen. Hundreds or thousands of truly innocent people, people with no connection to AQAP or al-Zawahiri at all, would have been killed. Nothing the USG does is more damaging than sending ground troops.
Options (1) and (3) had potential death tolls in the thousands. Option (2) had a death toll in the low teens.
I think reasonable people can obviously disagree about which of these options was the most prudent. But I don't think it's reasonable to suggest that there wasn't a difficult decision here; that the President, whose foremost duty is to protect the people of the US, could casually have chosen to leave al-Awlaki to his own devices. I look at the situation and thank God I'm not the President, and can instead retain my humanity.