"The plot also underscores that the Obama Administration is right to target Awlaki and other al Qaeda leaders in Yemen with Predator drone attacks, rather than merely issuing a criminal arrest warrant. Awlaki is actively plotting to murder Americans, and stopping him is an act of self-defense. The attempt by the ACLU and Center for Constitutional Rights to thwart these attacks in a lawsuit could get Americans killed."
Making sure that the American government can't arbitrarily order the execution of an American citizen will get Americans killed, basically. For what it's worth, the ACLU and the CCR aren't actually asking that Awlaki's life be spared. They're asking that there be due process:
The groups charge that targeting individuals for execution who are suspected of terrorism but have not been convicted or even charged — without oversight, judicial process, or disclosed standards for placement on kill lists — also poses the risk that the government will erroneously target the wrong people. In recent years, the U.S. government has detained many men as terrorists, only for courts or the government itself to discover later that the evidence was wrong or unreliable.
Al Qaeda is bad. Awlaki may well be a bad guy. But laws and constitutions are the ways civilized people balance the dangers of the world -- including bad guys -- against the liberties and rights of citizens. There is always risk. The government should have to have a high standard for putting one of its citizens on an assassination list.