The Cosmic Being that keeps the Federation in working order keeps an entire race under the delusion that they are not Too Dumb to Live; An entire race has been reduced to some Cosmic Being's pet gold fish.
Alternately, the Federation is hiding behind the protection of that Cosmic Being so they don't have to change elements of their civilization that are just plain broken.Which is just about everything.
Or: An entire species that is just too idiotic to realize that, when a Nigh Invulnerable, God-like, cosmic entity with unimaginable wisdom at it's disposal tells you that you really need to make some changes to the way they have been doing things, you should probably do so. The Cosmic Being literally devotes nearly all of it's spare time just to keeping their absolute mess of a government/educational system/legal system/EVERY FREAKIN' POSSIBLE FACET OF THEIR SOCIETY AND CULTURE from collapsing in a fiery heap of shame and failure. Again. The only change that has occurred in their society in 400 years of interstellar exploration is that the smart ones actually have an opportunity to leave their steaming failure of a society before it finally self destructs.
The scariest thing about the entire scenario is that, the higher up the command chain you go, the greater the incompetence of the people in charge. Looking at the crew of the Glorious Undertaking, and their entire civilization, is like looking at the The Dilbert Principle in action: the most incompetent people have been elevated to the highest offices, while the most competent are stuck at the lowest levels. This is most likely due to the fact that those who support the flawed ideals of the ruling regime are the ones who decide who gets promoted, so those who support the ruling regime are the only ones who get promoted. And since only an incompetent idiot would fail to see that the system is not working, only incompetent idiots get promoted. Meanwhile, the failing system is held together by the incredibly competent people who spend their entire lives at the bottom of the ladder.
The crew of the Glorious Undertaking sit idly by and watch as a comet strikes a planet full of sapient (but Bronze Age tech level) sophonts. They made no effort to aid, evacuate, or rescue the inhabitants... and they cite the Prime Directive as the reason why they didn't make a move to aid anyone. Now, feel free to go try and watch any episode of Star Trek: The Next Generation where The Prime Directive is a major theme without cringing, because this very closely mirrors more than one episode where the Prime Directive hindered the crew of the Enterprise in helping less advanced races in surviving situations that would be an extinction level event.
The crew of the original Enterprise would have likely attempted to divert the comet: the Prime Directive prohibits direct interference in the development of a sentient species, but it does not prohibit stopping an outside force from causing the annihilation of a species (in this case the gigantic comet). However, by the time of the Next Generation, the Federation had flown so far up its own philosophical arse that Picard and his staff spent days debating on whether or not they should save a planet full of sapient creatures from exploding or whether that would be thwarting the grand cosmic design.
The Coldest Equations chapter takes all of the fridge horror of The Cold Equations story, and turns it into a court case: What kind of a society would impose a death sentence penalty for stowing away on shuttles with zero security, literally no margin of error for said shuttles, and cut the shuttle's operating parameters to the point that there literally wasn't even room for a co-pilot? The space shuttles used by the Parodians would not, by 20th century standards, be cleared for flight about 1,000 feet!