The trial in New York of Ahmed Ghailani, the first suspect from the Guantanamo Bay, Cuba prison to face a jury in a U.S. criminal court, is being closely watched as a template for future terrorism cases and by those who think those suspects should be in military courts instead.

USA-GUANTANAMO/GHAILANIGhailani, a Tanzanian, is accused of participating in the 1998 al Qaeda-sponsored bombings of the U.S. embassies in Tanzania and Kenya, which killed 224 people. He was arrested in 2004 in Pakistan, and was subsequently taken into CIA custody for two years before going to the Guantanamo prison.

Many Republicans and some Democrats have said civilian courts are not up to the challenge of prosecuting terrorism suspects and favor the military commissions.

That fiery debate made its way into the trial on Thursday in the form of a lengthy footnote near the end of a 60-page ruling that barred a key witness, Hussein Abebe, from testifying. He is believed to have sold Ghailani the TNT explosives used in the bombings.

Judge Lewis Kaplan, defended his decision to bar the witness — because he had only been discovered after Ghailani was coerced to reveal his identity — and said a military commission judge would likely have made the same call.