George Washington University law professor Jonathan Turley said the criminal trial derailed the government's long-publicized assertions about Holy Land.
"From the beginning, the allegations were highly suspect and only got worse," said Turley, who has handled a number of national security cases.
Indeed, Turley said, if the government had begun with the troubled criminal case, it might never have succeeded in closing down the foundation administratively because its disputed evidence would have come to light years ago.
Such criticisms echoed those of Holy Land lawyers who had long complained that the charity was railroaded out of existence without due process of law and based on secret evidence.
"Before a person's domestic pet can be taken away for being vicious, they are at least entitled to a hearing. So what happened to Holy Land wouldn't happen to a dog," John Boyd, one of Holy Land's lawyers, said in an interview more than a year before the court imposed a continuing gag order.
Ironically, the government's decision to seek criminal sanctions may have succeeded most in exposing weaknesses in the administration's overarching case against Holy Land. Georgetown's Cole said prosecutors failed to produce evidence that the charity provided "one penny to support terrorist activities."
And in the end, despite years of FBI surveillance, wiretaps and seized documents, the case presented in court largely came down to conflicting testimony between an anonymous Israeli security official and a former American diplomat over which neighborhood charities in the Gaza Strip and West Bank were or were not affiliated with Hamas.
The government's allegations not only proved unpersuasive but engendered skepticism among some jurors.
"The whole case was based on assumptions that were based on suspicions," said juror Scroggins, who added: "If they had been a Christian or Jewish group, I don't think [prosecutors] would have brought charges against them."
An entrenched political, social and military organization among Palestinians, the Islamic militant group Hamas has long been an adversary of Israel and has been designated a terrorist organization by the U.S. since 1995. Last year, it won Palestinian parliamentary elections and now controls the Gaza Strip, home to 1.5 million people.
A White House spokesman declined to comment about the government's actions against Holy Land and referred calls to the Department of Justice, where a press official said he was precluded from making statements by the judge's gag order.
