See the episode Pen Pals. The population is going to be destroyed by a geological collapse, and Picard decides that the Prime Directive requires they let everyone there die. Of course, by sheer luck they hear a girl call for help to Data while they are debating the issue, which Picard determines is a "plea for help" so doesn't violate the Prime Directive if they respond. But without that plea, they were going to let everyone die (even though they had the technological capability to save the world without anyone knowing they intervened). I believe this episode had the most protracted discussion of the Prirme Directive that we have seen in-fiction. In Homeward Picard considers it a grave violation of the Prime Directive that Worf's brother has attempted to save a population when everyone on their planet was going to die in 38 hours.
OK, you have a point, sometimes it does not mean what I thought it did. If you look at the general description of it, however, there are 8 items there, only one of them ("Helping a society escape a natural disaster known to the society, even if inaction would result in a society's extinction.") of the questionable type you describe. The original statement, "no identification of self or mission; no interference with the social development of said planet; no references to space, other worlds, or advanced civilizations." also makes perfect sense.
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?