Yes, the military can and should target American al Qaeda members
Before I explain, let’s remember that — legally — we are in a state of armed conflict against al-Qaeda, pursuant to the post-9/11 Authorization for Use of Military Force. We are not engaged in a law-enforcement operation. In other words, attacking a member of al-Qaeda is more like attacking a member of the Viet Cong in the aftermath of the Tet Offensive than it is like attacking American member of a Columbian drug cartel. An American who’s drug-running in South America is entitled to all the individualized due process of any citizen and certainly cannot be summarily killed by drone strike. An American member of al-Qaeda is, by contrast, is in a state of open and declared warfare against the United States, a state of war acknowledged by both parties to the conflict. …
In the current war, we go to great lengths to avoid targeting the wrong individual (when I was in Iraq, our targeting decisions were typically based on multiple, overlapping pieces of intelligence). Killing the enemy while sparing civilians is sound counterinsurgency, and it is sound morally. But when civilians do die, the responsibility for their deaths lies with the enemy that unlawfully used them as human shields.
If all this sounds harsh, or “chilling,” or scary, that’s because it is. War is hell. And there is no constitutional doctrine that exempts American citizens from that hell when they choose to wage war against their own country. Any other legal doctrine will create yet another perverse terrorist incentive: Can an American terrorist now be a unique human shield to prevent direct attack?