Hannigan acknowledged that someone else would quickly step into his shoes.
"It would have been strange to see this as a massive breakthrough," he said. "The (Isis) threat went on."
Douglas Wise, who helped oversee the CIA's Middle East operations, added: "If you look at Emwazi as an adversary, he certainly wasn't a glorious battlefield commander.
"He wasn't high in the hierarchy, such as it was, but he was a powerful and credible adversary nonetheless. Why? He was from us. He was of us. And so he knew us instinctively.
"For us, this was as personal as if he'd been an American citizen."
The Channel 4 documentary, previewed by the Sunday Times, details how the security services compared the video released in August 2014, when US journalist James Foley was beheaded, with archive photographs and voice recordings of phone taps held by MI5 and Scotland Yard.
But the hunt was far from easy. Emwazi, who had studied computer science at Westminster University, wiped clean every computer he used every time he sent or received a message to safeguard it from bugs.
"He used a whole series of commercially available products to obscure his identity, including very strong encryption and virtual private networks," Hannigan said.
"Any one of those products would have been very difficult for an agency to tackle. What he was doing was layering them on top of each other."
But his weakness was his desire to keep in touch with his wife and child - believed to have been in Iraq at the time - helping intelligence officials track him.
Colonel Steve Warren, then Pentagon spokesman, said: "He was very careful about his actions. But you know what? They all slip up eventually."
When they received intelligence about Emwazi's movements one night in November 2015, a drone was dispatched to follow his car. After 45 minutes, Emwazi emerged from the vehicle.
"You can't see his face but we could sort of see how he moved, the cut of his jib, so to speak," said Warren, who was watching a live feed.
"The angle of his beard, these things we could see. Eventually we were convinced that this is Jihadi John. And so the floor commander at the time orders, 'Take the shot'."
Within 15 seconds Emwazi was dead.
The Hunt For Jihadi John will be broadcast in Britain on May 20.