On foreign or U.S. soil, if you're in the act of waging war against the U.S., and in the line of duty to protect themselves, agents of the government, such as the military, happening to kill a Citizen does not pose an issue to me. No more than if a copy shoots and kills a bank robber whose in the process of robbing the bank and is threatening people with a gun.
On U.S. soil, outside of the above situation, the attempt should be to arrest...not kill...an individual intimately involved in a significant position within an organization waging war against the U.S.
On foreign soil, outside of the above situation, I do not have issues with the U.S. military treating said individual as they would any other militaristic target if that individual is in a strategic position within an entity at war with the U.S.
What I mean by that is....would we normally launch a special forces stirke force to go after random al-qaeda grunt #2458? No? Then its not okay to do such a thing if random Al-Qaeda grunt #2459 is a U.S. citizen. However, if we would normally do a special strike force attack on random high up AQ leader #6 in Afghanistan, then I have no issue doing the same thing if random high up AQ leader #5 is a U.S. Citizen.
If you've assumed a leadership position, outside of this nation, with an entity indisputably engaged in war with the United States you should not be granted the privledge of being able to pose a greater harm to the United States and its population by being essentially untouchable. IF apprehension in such a strike is possible, then that should be the first option, but I have no issue with the result being death in such a strike if capture is not a reasonable probability without significantly raising the threat to the lives of our soldiers.
We are innocent until proven guilty, yet if someone was taking a shot at the President I'd have no issue with a secret service member unloading 8 rounds into the guys chest long before there's any trial "proving" his guilt. I see having an active leadership type of position, outside of the country, with an organization that is unquestionably at war with our government as being on a very similar level.