There does have to be rules about how this is used. Very stringent rules. However, if someone is actively working with others to kill Americans and damage our interests, and is hiding in a place that does not honor a warrant for arrest, or where we have no method of getting him out without losing people of our own, then we should take him out whatever way we can. And drones are a very good tool for that.
What if Timothy McViegh had found refuge among a people that would not give him up, and let him continue to work toward killing more Americans? Would you have say, "Do nothing to him because he is an American Citizen"?
People who actively plot terrorist attacks against the US need to know that there is no place in the world where they are safe. That death can rain down on their heads any time, any place.