If those enemy combatants are U.S. citizens, and if we know their name and are specifically seeking them out, then we should charge them to preserve the efficacy of the Constitution.
Ordering the death of a specific person because it would be too messy to charge him is making a mockery of due process.
We didn't kill Awlaki because it was "too messy". We killed him because it was the best way to reach him in Yemen, where he was hiding out.
Once gain, Awlaki knew the government was after him for two years, he did nothing to change his fate. He didn't even change his tone.
If I align myself with the terrorist group responsible for the Cole, 9-11, Khobar Towers, Ft. Hood, and a multitude of other events, I wouldn't expect any quarter to be given on the battlefield simply because I am an American citizen.