It was perhaps the most successful single strike in the history of America's controversial unmanned drone programme. Not only did the attack in Yemen kill firebrand American-born cleric Anwar al-Awlaki, but it also appears to have silenced one of militant Islam's best known propagandists and one of the world's most feared bomb-makers.

Samir Khan who, like Awlaki, was an American citizen, is now believed to have also died in the missile strike as he travelled with Awlaki. Khan occupied a unique position in the murky work of al-Qaida in the Arabian peninsula (AQAP) as the editor of the sophisticated terrorist online magazine, Inspire. It is a vital recruiting tool for AQAP, as well an effective way of touting its beliefs in English. Khan, who grew up in North Carolina, brought his expertise with computers to the website as well as his intimate knowledge of life in the west.

Killing Khan alone would have been a significant achievement for the CIA-operated drone programme. That he was killed alongside Awlaki was double the triumph. But unofficially the US now believes that a third terrorist was also killed: Ibrahim Hassan al-Asiri.

Though his death has not been confirmed Asiri is also thought to have been travelling with Awlaki when the drone struck. Asiri is a master bomb-maker whose fingerprints were said to have been found on the device worn by the so-called "underwear bomber" who tried to blow up a plane over Detroit in 2009. He is also suspected of having made the bombs that AQAP tried to ship to the US last year using postal services, and disguised inside printer cartridges.

Christopher Boucek, an expert who has studied AQAP and Yemen, told the Associated Press that the suspected death of Asiri was so important that it could "overshadow" the deaths of Awlaki and Khan. Asiri, 28, a Saudi Arabian engineer had fled to Yemen after being put on a list of his home country's most wanted terrorists. The strike, which targeted a vehicle in which the men were travelling in northern Yemen, has been hailed as a virtually "cost-free" victory in America's war against militant Islam.

President Barack Obama did not hesitate to praise the attack, calling it a "major blow" against al-Qaida. The news also provided a rare opportunity for senior Republicans running for the party's 2012 presidential nomination to heap praise on Obama.

Even Texas governor Rick Perry, a constant critic of the White House, hailed Obama. Mitt Romney, Perry's main rival, said: "I commend the president" as he called the attack "…a major victory against Islamist terrorism".

Yet, despite the three deaths and celebratory mood, the operation's impact is not as clear-cut as it seems. The killing of two American citizens abroad without even a token effort at judicial process is a potential moral and legal morass for both the White House and anti-terrorism officials alike. In a sign of the highly sensitive nature of the operation, Obama has declined to give any precise details of the attack and his role in the chain of command, which stands in contrast to the aftermath of the death of Bin Laden. "I can't talk about operation details," he told a radio interviewer on Friday, and then stressed the involvement of the Yemeni government in the strike.

But an outline of the long manhunt for Awlaki has started to emerge as well as an idea of how it ended. In April of last year, Awlaki's status as a significant terrorist inspiration led Obama to authorise US forces to kill the preacher on sight. The decision resulted in the US military stepping up its hunt for a man who was second only to Bin Laden as a target. The operation was dubbed Objective Troy. Soon after the authorisation, there was an increase in the number of unmanned drones taking to the skies above Yemen's capital, Sana'a. But the move was provocative, especially with the mountain tribes who for generations had been hostile to rule from Sana'a and were angry at US interference.

Yet Yemen's government did help in the hunt, which was marked by near-misses as the elusive preacher became expert at dodging those who tried to capture or kill him. In May last year, a drone strike narrowly missed him.

Unlike most drone attacks in Yemen, this operation was controlled by the CIA, not American special forces. Flying from a new base somewhere in the Arabian peninsula, the drone took off to trail Awlaki after several days of surveillance had tracked his movements. Then, as his vehicle drove in the northern provinces, apparently after leaving a funeral, the drone fired a Hellfire missile destroying the vehicle. If it had missed, US aircraft with missiles were nearby. The operation is seen as deeply sensitive, given the near state of civil war in Yemen. But as Yemen's lawless interior can offer safe haven to many radicals, it is also seen by America as one of its highest priorities in the war on terror.

However, the real concerns lie in America. The extrajudicial killing of two Americans is a cause of concern for civil liberties campaigners. They argue that American law demands a fair trial for US citizens suspected or charged with terrorism activities, and that targeting them for assassination is illegal. They say that the drone programme that killed Awlaki and his companions is essentially execution without trial. "This is a programme under which American citizens far from any battlefield can be executed by their own government without judicial process, and on the basis of standards and evidence that are kept secret not just from the public but from the courts," said Jameel Jaffer, the deputy legal editor of the American Civil Liberties Union.

The debate over the move is so intense that the justice department has drawn up a secret memorandum supporting the targeting of Awlaki and arguing for it on legal grounds. The Washington Post newspaper reported that senior lawyers across the Obama administration had been involved in writing the legal advice. They have argued that killing Awlaki was justified because America was involved in a state of war with Islamic radicals. They say that means militants like Awlaki are effectively high level enemy soldiers who represent a real threat to US forces and so can be killed legally. Similar arguments were deployed by the administration of President George W Bush, who considered many Islamic militants "enemy combatants" who therefore could be treated outside the judicial system. That process frequently outraged many liberal commentators and some senior Democrats, but is now effectively being deployed by Obama.

It is an argument unlikely to satisfy legal critics. "It is a mistake to invest the president — any president — with the unreviewable power to kill any American whom he deems to present a threat to the country," said Jaffer.

His concerns were echoed by Vince Warren, the executive director of the Centre for Constitutional Rights. He said that the attacks essentially granted the US government the power to kill anyone it considered a threat, without having to prove in court why it had come to those conclusions. "If we allow such gross over-reaches of power to continue, we are setting the stage for increasing erosions of civil liberties and the rule of law," Warren said.

But there seems little political appetite to take on those issues. Ron Paul, a libertarian-leaning Texan Republican congressman was one of the few voices to speak against the killing of a US citizen. But, in general, reaction across the political spectrum was supportive.