[Postscript 2] In the letter's page of Captain America 328, Marvel backs down very slightly, by offering a vaguer response:
...we do not deny that enemy soldiers died because of Cap's actions. Still, Cap never regularly carried a gun, not was his mission to kill as many of the enemy as he could. His mission was to "destroy the enemies of liberty," which are the concepts of fascism, Nazism, and totalitarianism, not the individuals who espouse them. True, you cannot attack abstractions-- you can only attack the individuals who act in accordance with them. But its an important distinction. Further to the point, soldiers at war play by different rules than civilians at peace and Cap has had years to make peace with himself about his wartime actions. We're not saying that Cap is or ever was a pacifist, but he does have a profound respect for human life. It is a respect that has grown as he has matured, and includes respect for the lives of his individual enemies. Killing an enemy is always Cap's last resort, and every death he's ever been responsible for has taken its toll on his inner peace.
[Postscript 3] A more detailed critique of the way Marvel handled the storyline where Cap killed a terrorist, and the events that followed, from the letter's page of Captain America #329: