"With the assistance of Khan's network, countries could leapfrog the slow, incremental stages of other nuclear weapons development programs," the State Department alleged when it slapped its first sanctions on Khan last month.
The extent of Khan's international network and the sheer physical presence of some of the materials he sold have led many to believe he was supported by the Pakistani state, something the government have vociferously denied. Khan himself claimed he had sold equipment to North Korea with the full knowledge of the military, then headed by President Pervez Musharraf.
"These centrifuges weighed something like half a ton each. You can't put them in your coat pocket and walk away with them," Hoodbhoy said. "It obviously involved a lot of official support. ... If there were aircraft of the Pakistan air force that flew these centrifuges out -- well, obviously there had to be somebody at the top who was also involved."
It was not clear whether Khan would be allowed to travel completely freely. He told journalists he would have to seek permission to travel outside the country and said he was free to move around inside. His wife told reporters that the government still held his passport.
But the court ruling that freed him has been kept secret. According to people who had read it, the ruling was particularly short and referred to an agreement not included in the ruling itself and so far kept out of the public view.
Asked about the conditions of his release, Khan told ABC News, "No conditions. Only have to take care of the security."
Khan lives next to a house full of intelligence agents who keep a very close watch on him, and throughout the news conferences today, intelligence agents were always just a few steps away.
It was about noon when Khan sauntered out of his home to greet a group of waiting journalists, stopping to pet his dog before casually answering questions. He looked relaxed and was about to start a third news conference in less than an hour when he received a call on his mobile phone.
The caller, reported to be the Interior Ministry chief, seemed to tell Khan to stop speaking to the press: After the call, Khan declined to answer more questions and returned to his house, leaving reporters on the other side of the gate.
Around Islamabad, though, residents were more than happy to praise a man each called a "hero." Many also praised a government whose policies have become increasingly popular lately.
"If we didn't have an atom bomb, would we have been so secure?" asked Reza Mohammad as he shopped for food in an Islamabad market. "America would have eaten us like Iraq and swallowed us like Afghanistan. India would have been sitting on top of our heads. We have two powers protecting us. One is Allah. And the other is atomic power."
Asked whether he was proud of everything he had done, Khan did not hesitate to answer.
"I will always be proud of what I did for Pakistan," he said. "Always."