The problem of habeas corpus isn't to protect Al Awalki, it is to prevent the government from torturing Al Avalki for ten years and then saying, oops, we got the wrong guy.
I absolutely agree that if Al Awalki was being detained by the government on American soil, he would have been entitled to file a habeas petition to contest his detention. Absolutely no doubt, and there was an 8-1 Supreme Court decision just this decade, post-9/11, that reaffirmed this principle. Habeas is the bedrock of our civil liberties and we should guard it jealously.
But habeas is a procedure for challenging illegal detention, meanwhile Al Awalki was a fugitive. He was not in the hands of U.S. authorities, on U.S. soil. He took up arms against America in Yemen, and was hiding, evading capture. Habeas is inapplicable to a person who is evading the government's attempts to bring him to justice, in effect evading the government's attempts to give him due process. It is inapplicable by the very nature of the device--a writ from a court to order the release of a prisoner being held by an executive authority within the court's jurisdiction. No U.S. court had jurisdiction over Al Awalki.
These guys always assume the government only takes freedoms from the bad actors, but, that logic is completely circular. The entire point of our system is that the government doesn't get to make that determination unilaterally. When they do, and in particular when the Executive alone does so, it's called a dictatorship.
