The Obama Administration’s counterterrorism policy just received a terrible setback. After a five day jury deliberation only a few blocks from where the World Trade Center towers once stood, a civilian jury decided to convict a known Al Qaeda operative on a single count of conspiring to destroy American government property with an explosive device.

The defendant in question was a man named Ahmed Khalfan Ghailani who law enforcement experts believed played an instrumental role in Al Qaeda’s 1998 suicide bombing on American embassies in Kenya and Tanzania. Some 224 people were killed on those attacks, among them twelve Americans.

According to American counterterrorism officials, Ahmed Ghailani was one of the operatives involved in the plot. Throughout the trial, New York prosecutors claimed that he personally bought the explosives that were used in the attack, then skipped town to Pakistan once the operation was orchestrated. He has been on the American government’s terrorist list since. Pakistani authorities managed to capture him only six years later when he was subsequently transferred to a CIA interrogation facility for questioning.

So after all of this evidence, why was Ghailani convicted on just one count?Or, to put it more dramatically, why was a member of Al Qaeda acquitted of 284 other charges, including murder, conspiracy to commit murder and terrorism?

Part of the answer concerns the lack of evidence directed against Ghailani in the first place. There was a whole lot of speculation as to his involvement but the actual proof was hard to come by. The star witness in the trial — a man named Hussein Abebe who claimed to have sold Ghailani the explosives — was excused from testifying by the presiding judge. That left a wide gap in the prosecutor’s case.

Something else that could be responsible is the nature of civilian trials in general — something that Republicans and New York legislators have been consistently hammering the Obama Administration on.

In contrast to military tribunals or military commissions that handle the bulk of war related crimes, civilian courts are governed by strict rules that provide defendants with a whole range of rights. Whereas a military commission may have permitted evidence based on CIA interrogations, civilian trials are more inclined to throw that evidence out. This is precisely what Judge Lewis A. Kaplan did with respect to Ghailani, arguing that he was tortured numerous times by the agency throughout his detention.

In the end, the trial will probably be seen as a failure by most. A terrorist being declared innocent on 284 charges while being convicted of only one leaves a bad taste in the Obama Administration’s mouth, particularly since the president has stressed his intention to continue to try captured terrorists through the regular court system.

In the end, justice was in fact served. Ghailani faces a minimum of twenty years in federal prison, with the possibility of a life sentence during his January 25 hearing.

The result wasn’t pretty, but the civilian courts did their job, convicting a killer on the one hand while upholding the rule of law in the process.