There comes a time when America must guard itself against threats from enemies, both foreign and domestic. Just because the threat to the country happens to be America does not mean that the United States should sit back and allow itself to be in danger. Severe action must be taken to protect ourselves.
The first and main reason for the existence of any and all governments around the world throughout history is for the well being and protection of the people who live within the nation, a nation killing its own citizens can only ever be justified under extreme circumstances (police officer defending themselves in a shootout with criminals, capital punishment [something I don't personally agree with, but a good example non the less] etc...), assassinations against a nations own citizens assumes that these people are neither proven lawbreaker nor are they an immediate threat to others, and that they are being killed for political reasons (or other other reasons that are basic rights in most modern western societies). My argument doesn't solely apply to American citizens/ government.
No it is not okay for the government to assassinate an American citizen. There is no justification to this action because a new question will arise. What next? If a government can justify a murder/assassination, you are allowing the government to have limitless power. Any government does not have the authority to decide whether someone gets to live their life or not.
It is never considered justified for a government to assassinate one of its citizens. The death penalty is the harshest punishment that a government can exact upon one of its citizens. The assassination of a US citizen does not even meet the definition of the death penalty, seeing as there is no court of law involved.
It is the government's job to protect it's citizens, not assassinate them. If someone is deemed to be a risk to others or to national security, they should be arrested and afforded due process. Killing someone is never the solution, and should not be entertained by any civilized government, regardless of the crimes that person may have committed.