Killing Joker means, in some sense, Batman had to agree that Joker's ethics -- killing your enemy to advance your ends -- work.
At least in The Dark Knight, the Joker was an outright nihilist. His primary goal was simply to prove that everyone is as crazy as him underneath.
Mind, the whole supposed Moral Dilemma about Society on the Brink of Collapse should anyone ever See Through the Noble Lie and realize that the Joker Was Right and there really is just Nothing... well, it kinda goes away once you confront the abyss yourself and realize that, given a blank canvas, you'd prefer to paint a pretty picture than burn the building down.
(Or in other words, the Joker presumed to prove that people must be Nihilists like him underneath, without considering whether the result might not be a heavily-armed batch of Existentialists.)
Disclaimer: I am not a philosopher, so this post will likely seem amateurish to the subject matter experts.
LW is big on consequentialism, utilitarianism and other quantifiable ethics one can potentially program into a computer to make it provably friendly. However, I posit that most of us intuitively use virtue ethics, and not deontology or consequentialism. In other words, when judging one's actions we intuitively value the person's motivations over the rules they follow or the consequences of said actions. We may reevaluate our judgment later, based on laws and/or actual or expected usefulness, but the initial impulse still remains, even if overridden. To quote Casimir de Montrond, "Mistrust first impulses; they are nearly always good" (the quote is usually misattributed to Talleyrand).
Some examples:
I am not sure how to classify religious fanaticism (or other bigotry), but it seems to require a heavy dose of virtue ethics (feeling righteous), in addition to following the (deontological) tenets of whichever belief, with some consequentialism (for the greater good) mixed in.
When I try to introspect my own moral decisions (like whether to tell the truth, or to cheat on a test, or to drive over the speed limit), I can usually find a grain of virtue ethics inside. It might be followed or overridden, sometimes habitually, but it is always there. Can you?