You're writing a story seemingly complaining about something that never happened, and never would have happened.

And honestly, I really don't know where you're going with the rest of this post. If you don't feel like a goodie should kill neutrals, then don't kill them. It's pretty simple, and I would say most (but not all) good aligned characters make that same decision.

So again.. I don't know what you want.

But basically you wrote a story complaining about how you were dumb, and somehow it's other people's fault and I think that's a terrible story.