Following the line of argument in the article would mean that Lincoln ought to have sought to indict each member of the Army of Northern Virginia.
If you wage war against the United States you're an enemy combatant and may be killed anywhere at any time prior to a cessation of hostilities.
And: if we actually had a President who was willing and able to get the US Armed Forces and the CIA to kill Americans at will in the United States, does anyone think a court order would put a stop to the practice?