In civilian court, shouldn't the case against KSM be thrown out?

So I imagine it doesn’t make any difference for the civilian legal system if John Doe is suspected of a single cruel murder or Khalid Sheikh Mohammed is suspected of organizing the murder of thousands of people. If this is true — and it must be true — I imagine what would have happened if John Doe had been held six years at a military detention camp without the normal rights given to him by the system, had been waterboarded 183 times (a form of torture, according to the president), and accordingly confessed without having had the chance to use his Miranda rights, which never had been read to him.

In order to protect the purity and autonomy of the American legal system, shouldn’t this case against the suspected terrorists be tossed out by the judge? If I were to be the judge at the criminal case against KSM, I would not have another choice, I imagine…

Which brings me to another question: If [Obama and Holder] know what I know, why did they do it? Is it really only to demonize Bush — the prosecution has to share all kinds of sensitive information with the suspects — and to project the misery of the present economic situation and the dangerous stagnation in Afghanistan on the previous administration?