Were dead Confederates US citizens?

Since your OP is a relatively obvious attempt to make commentary upon the recent killing of the al-Qaeda leader who was an American citizen, let’s address the OP in proper context. It has never been unconstitutional to kill a citizen during time of war when that citizen is engaged in war acts against our country. The issue was addressed more than once by courts during WWII. Citizens engaged in acts of armed rebellion against the US would not be entitled to be arrested and tried for their crimes, rather than shot during military conflict.

Or, if you wish to think of it this way, when you are engaged in a military action against the government, being shot by the loyal soldiers is “due process.”

Now, if the soldiers of the United States happen to run across Johnny Reb while Johnny Reb is on leave at home, plowing the family farm, and shoot him without arrest and trial, that might well be a different story. Of course, that’s not what happened to our al-Qaeda American, either.