1. Assume for the sake of argument that imprisonment of suspected terrorists without trial violates the Fifth Amendment. The question then becomes: What must the government
do about the violation --- that is, what is the prisoner's
remedy?
A) The canonical remedy for unlawful imprisonment is the writ of habeas corpus [1]. When a court issues "the Great Writ," it orders the prisoner's jailer(s) to bring the prisoner to court and, by implication, to release the prisoner if the court so directs.
B) Article 1 of the Constitution expressly empowers Congress to suspend habeas corpus --- in other words, to strip from courts the authority to order the release of prisoners --- "when in Cases of Rebellion or Invasion the public Safety may require it." [2] Nothing in the Fifth Amendment alters this congressional power of suspension.
C) It might be argued that in enacting the Patriot Act, Congress partially suspended habeas corpus in response to the "Invasion" we call 9/11.
D) The courts try to interpret the various parts of the Constitution to be in harmony with one another if at all possible.
E) So, "properly" interpreted, the Fifth Amendment might not stand in the way of imprisonment without trial in a case covered by a congressional suspension of habeas corpus. (The breadth of this possibility troubles me, incidentally; also, I'm far from a constitutional scholar.)
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2. As to whether the Constitution prohibits killing an enemy combatant in wartime without individualized due process in each case: That'd be a really, really tough sell, not least because if that principle had been followed, the U.S. would not long have survived as an independent state.
[1] http://en.wikipedia.org/wiki/Habeas_corpus
[2] U.S. Const., art. 1, sec. 9, http://www.usconstitution.net/xconst_A1Sec9.html