The kidnapping was discovered and linked to the CIA by Italian authorities due to "sloppy" tradecraft, according to U.S. officials. Much of the evidence used in the trial involved cellphone records of the CIA team assembled to take Abu Omar.
"They were using e-mail, they were calling home, the Italians were able to connect their credit cards with true names and true addresses," said former CIA officer Bob Baer.
"I did these same things under the Reagan administration," Baer told ABCNews.com "When we did a rendition, we did it in international waters. The Bush administration threw all caution to the wind."
The operation to capture Abu Omar was part of the CIA's extraordinary rendition program, according to U.S. intelligence officials involved in his transfer. The kidnapped cleric was held in Egypt for four years and says he was repeatedly tortured there by Egyptian interrogators.
He was never charged with a crime and ultimately set free. He remains in Alexandria, Egypt.
"He was the wrong guy," said Baer. "It was not worth putting the reputation of the United Sates on the line going after somebody like this."
According to both U.S. and Italian intelligence officials, the trial ruined the relationship between the two countries' intelligence services, and has hurt continued counterterrorism efforts.
DeSousa who resigned from and brought a lawsuit against the U.S. government fears the damage to U.S.-Italian relations from the verdict will continue.
"It's getting more embarrassing every day," deSousa said.