Shinji killing an Angel is the worst case scenario?
The situation with Kaworu is a bad example because it's a true dilemma: kill your best friend and save humanity but live with the guilt, or let your best friend live (against his request) and condemn all of humanity. Kaworu isn't a victim of Shinji's autonomy, as you claim, and this isn't an example of the bad things Shinji is capable of doing because of Eva. If anything, it is an example of the bad things Shinji has to go through because of Eva, like an analogy for life. "I musn't run away", "Why do you pilot Eva?" etc.
Anyways, this seems to be going in circles and we're beginning to focus too much on the original series. If this isn't going anywhere, perhaps we should shift our focus to other points more relevant to NTE?