"Wow, they should definitely put a bullet in that guy's head ASAP,"
Consider the comparable real life situation. LessWrong has a policy against listing real life examples, so I won't, but you should be able to think of some. While we're at it, think about the reason LW has this policy.
"Wait, what's the big deal, I don't see anyone getting hurt here,"
You mean you don't see anyone getting immediately hurt. With the kind of civilization affecting decisions that occur on star trek frequently have indirect effects that are orders of magnitude larger than their direct effects.
Consider the comparable real life situation.
The problem is that fiction often removes the most compelling reasons that this sort of thinking doesn't work in the real world (uncertainty regarding facts, uncertainty regarding moral reasoning), but tries to retain the moral ambiguity. I think I would be much happier if police were perfect virtue ethicists or deontological reasoners than is currently the case, but if Blofeld reveals his dastardly plans to Bond, I want as many bullets in his head as can be arranged in short order.
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?