Nov. 17 (Bloomberg) -- A criminal trial in civilian court for admitted Sept. 11 mastermind Khalid Sheikh Mohammed is bound to be messy, expensive and fraught with pitfalls.

At least it isn’t a military tribunal.

In the years since the murderous attacks on New York City and the Pentagon, the concept of military commissions has been so thoroughly discredited that they have come to represent a detour around justice, not a pathway to it.

Military prosecutors who resigned from the commission in protest bolstered critics’ claims that the tribunals were designed to ensure convictions regardless of proof, not to offer real due process as American standards demand.

Attempts by the Bush administration to design military tribunals that would pass constitutional muster utterly failed, the U.S. Supreme Court ruled in 2006. Nor was the court entirely happy with revisions Congress made to the tribunal law after 2006.

In almost eight years since President George W. Bush first signed an order creating military commissions, only three people have been convicted before them, so persistent have been the legal challenges and murky their legal standing.

Now the Obama administration, working with Congress, has amended the process again, granting more rights to the accused to make the tribunals more consistent with American principles of justice.

Fewer Differences

So now there are fewer differences between a military tribunal and a civilian court. Evidence obtained through torture or otherwise “inhuman or degrading treatment” is rightly barred in military commissions, as it is in civil court.

The differences that remain between military tribunals and civilian courts mostly make federal courts the superior venue if the goal is a fair trial.

For starters, military commissions are still part of the executive branch, whereas the judiciary is a separate, independent branch of government. That’s important given evidence of past political interference with the commissions.

Hearsay evidence is presumed unreliable in both venues, but stands a better chance of being admitted in the military tribunal. That may give prosecutors a better chance at conviction -- and an unfair advantage.

Yes, a high-profile criminal trial can drag on interminably while a military court could work faster. But it’s also true that federal courts have been conducting trials of terrorists for years and know how to handle them.

Trade Center Bombers

The 1993 World Trade Center bombers were convicted in the Southern District of New York, where Attorney General Eric Holder wants Mohammed tried. And since the Sept. 11 attacks, more than 100 people accused in terrorism-related cases have been tried in federal courts.

This means that many issues unique to such cases have already been hammered out. It means U.S. jails and prisons have successfully held the most dangerous of criminals and continue to do so.

Precisely because the latest iteration of military commissions is new, it will take years for its procedures to be resolved through litigation.

As for handling classified information, the new military commission law copies procedures used in civilian courts. In either venue, a judge decides whether classified information is relevant to the defense and whether a scrubbed version of it would satisfy the defendant’s fair-trial rights.

National Security

If, after that, the government still claims national security would be harmed if certain classified information were presented, the government has to choose between that risk and continuing to prosecute. And that is true in both courts.

The biggest advantage to using federal courts in this case is because it’s a public forum which promises the accused due process, no matter how despicable the crime or how solid the evidence of guilt.

President Barack Obama and Holder imply that military commissions, even the revised ones, are still inferior to civilian courts when it comes to protecting the rights of the accused. They do so by suggesting that they will decide which detainees will be tried where, depending on the evidence.

No doubt this means that Holder is absolutely confident of convicting Mohammed in federal court and has taken into account the considerable hurdles the prosecution faces. That’s a relief.

But any fair system carries with it a risk of acquittal. And if the administration is setting aside one court system for cases where the evidence couldn’t stand up to the rigors of a civilian court, then it shouldn’t use military tribunals at all.

By allowing the torture of terror suspects, detaining them indefinitely on what the White House hoped would be a legal black hole and offering no fair way for them to show their innocence, the U.S. lost whatever moral authority it once had in the area of human rights.

The decision to try Mohammed in federal court in New York sends the message that we are now working to regain some of that authority. How much clearer the message if Holder had abandoned military tribunals to the past, too.

(Ann Woolner is a Bloomberg News columnist. The opinions expressed are her own.)

To contact the writer of this column: Ann Woolner in Atlanta at awoolner@bloomberg.net.

Last Updated: November 16, 2009 21:00 EST