Are we Killing al Qaeda or Americans?

Recently there was the US government killed a US citizen by the name of al-Awlaki, a known al Qaeda member. The question is whether or not the government had the right to kill him. After all, he was a US citizen and therefore is protected by the government, supposedly anyways. Some libertarians are saying that we are becoming like the Soviets in how we are killing our own citizens in order to keep order, a police state. Republican Ron Paul said"If the American people accept this blindly and casually, that we now have an accepted practice of the president assassinating people who he thinks are bad guys. I think it's sad, Al-Awlaki was born here, he's an American citizen, he was never tried or charged for any crimes". The idea is that a citizen deserves the right to be tried as a traitor, for murder, etc, in court. I find this ironic in how Ron Paul is a republican and republicans are more gun-ho but here he is against the killing of a known enemy. To be fare, I agree but largely, I do not. He was a member of a terrorist group. I believe that if one, knowingly and willingly joins a group that one knows is out to damage the nation as a whole, he or she should be treated as any spy would have during the cold war. Spies are not tried in courts, neither were Germans in WW2 who moved from the US to answer the Fatherland's and the Fuher's call. I believe that war was declared and that means that the government is authorized to take the action to kill the enemy. I however do believe that if the opportunity had arisen that no lives were in danger and we could capture him alive, and then sentence him in court. However, under the circumstances I believe the Obama administration did the right thing.