The difference between me and Euphemia is that I, with all the training in the world, haven't killed anybody. Euphemia not only has but was in the process of actively doing it. Hell, one of the reasons why we imprison and execute prisoners is to prevent them from ever doing what they did again. Are you saying that this preemptive action is wrong?
Also, I have yet to actually give my true opinion about Euphemia's death in the context of the cartoon (in the context of real life we have but not for the cartoon). While I have said that Lelouch killed Euphemia to get her to stop, I didn't say I thought that she HAD to die (I already knew she was going to die in the first place; whether she HAD to or not has never really been my concern).
The thing with anti-heroes and Byronic heroes is that they exhibit qualities that we, as humans, can often relate to. Anger, confusion, self-hatred, self-destructive, struggling with integrity. These are things we can identify with. With Euphemia, there is not much to identify with, unless you are someone who is innocent, a pacifist and and naive to a fault (which you are not, by the way).
As I have said before, the problem with you is that you expect two sides, the "good" side and the "evil" side, and you don't expect these sides to touch. This doesn't even happen in Harry Potter or Star Wars, so its not going to happen in Code Geass (and it really shouldn't surprise you when it doesn't).
However, in MANY stories, the most thought provoking ones, the sides not only mix but sometimes indistinguishable. In Code Geass, the point is not really to find who the "good guys" and the "bad guys" are (this is something you figure out on your own) but noticing that the best of intentions can have evil in them.
The clearly good guy doing a clearly good thing to defeat the clearly bad guy who was doing a clearly bad thing is a story that has been told many times (Disney thrives on that sort of thing).