The Obama administration would love to avoid going to trial in the first military commission trial in Gitmo, but may be legally (not to mention politically) barred from doing so.
They'd like to reach a plea deal with the "defendant" (I use scare quotes because it offends my sensibilities as a lawyer to apply it to anyone held captive without the protections of the Constitution), Omar Khadr, because his case makes the whole process look as bad as it is. Khadr was a child soldier, just 15 when he was captured. He was heavily wounded when they found him, but somehow they determined it was him who threw a grenade that killed a U.S. soldier. A U.S. interrogator suggested that, if he didn't cooperate, he could be raped to death in prison. Nevertheless, the military judge let the resulting confession come into evidence. Then the Pentagon tried to ban journalists from Khadr trial because they had written about publicly-available information that the military nevertheless deemed secret. And an officer was excluded from the jury because he agreed with the President that Gitmo went against America's values and had hurt the country's international image.
The military is apparently surprised to learn that civilians consider it unsporting to coerce confessions from children by threatening them with rape and death, and then trying them in secret with a jury which excludes anyone who acknowledges reality. The Obama administration, being a little more enlightened, would like this case to go away. However, the Military Commissions Act forbids "unlawful command influence" on the process, which could be interpreted to mean that Obama can't order a more attractive plea deal be offered, much less dropping the charges.
For his part, Khadr, now 23, has rejected fairly sweet plea deals so far, saying "he was offended by what he saw as an attempt to 'legitimize the sham process' by dangling 'the least sentence possible' to coerce a confession. Good for him. I believe that the initial investigation was rigged anyway.