Even if everyone has perfect intentions (doubtful), you need checks and balances to prevent human error.
This is for better or worse.
Extra-judicial killings happen a lot. In the case of self-defense for example. "Cop thought the suspect had a gun" is a mistake that happens often, but it can be legitimate as well.
As for your other point, self defense is a long established affirmative defense for murder, yes. However that has nothing to do with the issue at hand.
If the government has a case to kill a citizen, that case needs to be made in court and evaluated by a jury of peers.
Well, the constitution is the rules and limits that apply to the US Government mainly (for the benefit of not only the US citizens).
However the Constitution is pretty much defined as the Law of the Land (Article VI https://en.wikisource.org/wiki/Constitution_of_the_United_St... )
And if the case is as you describe then it seems it's a case for a federal prosecutor to make in Court.
> "Where high-level government officials have determined that a capture operation is infeasible and that the targeted person is part of a dangerous enemy force and is engaged in activities that pose a continued and imminent threat to US persons or interests."
https://www.theguardian.com/world/2014/jun/23/us-justificati...
I fail to see the problem