So you're saying that extrajudicial killings, as in the case of bin Laden, may be acceptable, but that doing so based on secret evidence is a problem. I think that's a much easier case to make, though I think there's also a strong case to be made for secrecy in the name of national security. I think that if we had strong Congressional oversight and more powerful (but still secret) courts providing judicial review, the arguments against secrecy would be significantly ameliorated.
On the other hand, I don't see why citizenship is a moral or theoretical stumbling block. Does the killing become more moral or less problematic if it is the killing of someone who isn't a US citizen?
With all due respect, in practical terms this is no guarantee of anything stronger than hand waving. Diplomatic pressure, international courts, and treating perpetrators as mass murderers hasn't worked so well in, for example, the Bosnian context.
And again, would this have been an appropriate US response to the German invasion of Poland? France? Its assault of Britain? Germany wasn't even killing any US citizens.
Well, serial killers based in Afghanistan pose little danger to US citizens, and there is thus no imminent danger to US citizens. (Israel, on the other hand, has. Does this mean they could engage in US-style drone strikes in faraway lands without objection?)
On the other hand, there's nothing new about declaring war with someone. Armies are also killers, and al Qaeda is being treated as an army. Sure, there are differences, but those differences are because al Qaeda is not the typical uniformed, national army but a supra-national, un-uniformed opponent. If there is a new classification, it is because al Qaeda has deliberately chosen not to adhere to traditional classifications of combatants (and for good reason; they're much more effective operating as they do).