Great questions, and I totally understand where you're coming from in point "B." I am a lawyer and often times its my job to find ways to protect my clients' interests within the framework of the law. To find "loopholes" if you will. I think the bigger problem here is that I expect more of leadership. It isn't like the former administration needed anyone's permission to set up assassination teams to go after AQ. The EO's discussed above were not put in place by congress. They're orders that come from the oval office. If the president doesn't think they're good law anymore he can change or remove them at any time. It happens all the time. In fact, I really would have preferred that the administration had done this. As I mentioned above, I'm not really opposed to this tactic. But I really don't care for our leadership putting in place laws that really don't mean anything. If we're going to let the CIA assassinate bad guys, let's not pretend that we're not.
The bigger issue I struggle with is deceiving congress. On one hand, I think back to the 80's when congress and the CIA managed to cooperatively work together to fight a clandestine war in Afghanistan without it being on the front page. On the other hand, I agree with much of what has been said above in regard to the concern that congressional offices sometimes can't keep their mouths shut. This is even more disspointing than all of the shoddy legal work that came out of the Bush administration. The whole thing makes me wonder if there isn't a greater role for the IG when leaks do surface. It's such a shame that no one has been nailed yet for the Valerie Plame leak. I don't care if she was an actual operative as she claims or just sitting on a desk at Langley like some others claim. It ought to be a top priority whenever classified information of that nature is leaked, and the penalties should be severe. Normally I don't by very much into deterrance theories, but part of me believes that the leak problem would probably go away after one or two congressional staffers (or white house staffers - remember the Plame leak is believed to have come from the executive branch) were sent to prison for life.
This is a less compelling analogy, but does illustrate a couple of key points. Not only was the law different at that time, but the circumstances were different. Neither EO had been issued until the late 20th century, long after WWII. Additionally, Yamamoto was a military officer for a nation-state that was overtly at war with the US, who died in an ambush conducted by the US Navy.
This is a bit complex, but there are serious questions that haven't been resolved yet in regard to how the current "War on Terror" can and should be fought under the law (can you tell yet that I'm a big Rule of Law guy?). Today, we are in a global fight with AQ, which is a group that is neither a nation or a state. Congress has given the executive branch a tremendous amount of authority to prosecute this conflict under, inter alia, the 2001 Authorization for Use of Military Force (AUMF). In spite of this, there are huge problems because in some respect the language of the AUMF is so broad and ambigous that the government is still struggling 8 years later to figure out where the boundries of that authority are. In large part, this is an even more compelling reason why the Bush administration would have been in the green to go ahead with the assassination program in the absence of the EOs. So why hide behind lawyers?