Historically, how did we handle enemy combatants in the United States?

In the debate over this subject, the most ubiquitous of the examples of Americans killed fighting for the Nazis comes from the famous Supreme Court case of Ex Parte Quirin (1942). He is Hans Haupt, one of several Nazi saboteurs who infiltrated the U.S. in 1942 by secretly landing on Long Island and Ponte Verde Beach.

The interesting thing about that for present purposes is that, once ashore, they shed their uniforms. (By the way, Judge Mukasey had a very interesting explanation of why they did this in his district court opinion in the 2002 case of another American enemy combatant, Jose Padilla. See Padilla v. Bush (SDNY 2002), Op. p. 62 & n. 12 — link here.) When the Nazis were captured days later — by the FBI, not the military — they were wearing civilian clothes and not in the act of carrying out any of the terrorism they had plotted. Despite the fact that Haupt was an American and that the U.S. courts were open and functioning, FDR had them designated as enemy combatants, tried by military commission, and put to death (i.e., Haupt and five others, all German nationals, were executed; others who had cooperated were given lengthy sentences).