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I think the discussion was based on the assumption that the constitutional violations are so severe in these cases that conviction will not result in a normal proper US court of law. Otherwise, there is nothing to talk about, is there?
No. There's a difference between trial-level court and an appellate court reviewing a conviction.
What Obama is dealing with (or at least this is the hypothetical we are entertaining, because none of us really know for sure) are cases that might survive appellate review (due to overwhelming evidence of guilt), but would either be thrown out or severely damaged at trial level.
My point is simply that, under our rule of law, Constitutional violations are not an automatic get-out-of-jail-free card.