It seems to me that they would have construed it to allow taking enemy prisoners of war during a war. Wars, at that time were declared by Congress and has clearly defined victory conditions. Prisoners were expected to be repatriated at the end of the war.

Now we're engaged in hostilities not declared as a war and without clearly defined victory conditions. If enemies in that conflict are treated as POWs, their detention is indefinite. I'm pretty sure the Constitution's authors did not intend anything of the sort.