The funny thing is this episode actually features multiple potential violations going back centuries:
- the initial installation of the weather towers (though you could argue this might not be a Federation act, since it's implied a specific species was responsible and perhaps they weren't a Federation member, or the act preceded the formation of the Federation, though I don't think the latter is true since this is all tied to that one researcher's clue and I'm pretty sure they worked on the towers);
- the intent to fix the tower, which is arguably an intervention in the natural course of the planet and its civilization (but on the other hand could also be seen as making the best of a previous intervention on the planet);
- Michael revealing herself to the father, which is the most obvious violation.
There is a real argument that says the planet came under the care of the Federation as soon as those towers were installed and thus every act from then on has been a sort of attempt to limit the damage of that violation, therefore everything's fine. But thinking about it that way also a) highlights just how messy all this intervention business can be; who put those towers there in the first place knowing that they'd need maintenance and not coming up with a plan to ensure that happened? (though the Burn might've fucked with those plans) and b) mirrors arguably well-intentioned attempts by real-life nations to intervene in the affairs of others that went awry.
This actually reminded me of another idea I had to flip the antagonists. While I don't think the conflict in S4 worked out well stretched out across a full season, I do appreciate the fact that at least Booker has a very legitimate reason to want to act against the Federation and destroy the aliens. Instead of Breen love politics, they could have been up against Federation scientists or someone else who want to use the technology to intervene like the original scientist did on this planet, and thinks all life is worth saving and that it's ethically wrong to let people die because of a moral judgement that they are not ready to be 'saved'.
Rather than have Moll and L'ak completely absent from this episode, they could have done something similar to when Michael and Booker were forced to work together in S4 despite being on opposite sides, where the antagonist and the Discovery crew both recognize that these innocent people shouldn't die, but Michael has to struggle with the ethics of the Prime Directive rather than just have it be "paperwork" that she has to deal with.
Certainly violating the prime directive has happened several times before, but it's almost either a one off or a bad thing. But I feel like if they took the tact of the "eco terrorist" on TNG who blew herself up to prove that warp drive was dangerous and had a sustained antagonist who is has a defendable point of view and wants to get the Federation to understand that non-interference can be problematic... it'd be an interesting dichotomy at least.
This was an interesting thing to consider as well. It could potentially start a religious war, but a lot seems to turn on exactly who Michael revealed herself to, and what kind of a person he is. So much turns on how he absorbs and processes all the information Michael, Tilly and Culber have given him, not only about the nature of the universe and their place in it, but the information on how to maintain the tower(s). I think the episode guides us to the conclusion that everything works out fine; he comes to his people with a revised religious dogma, one that doesn't demand ritual sacrifices, and he has powerful evidence in the form of long-overdue, drought-ending torrential rains. But even then, I can't imagine everyone just goes back to the way they were except for that one thing about their core religious beliefs. Do they go and fix the other towers, now that they know it's not the will of the gods that made them inoperable? If they do, do they succeed and expand their civilization, or fail and bring it to the brink of collapse? And that's one of the better possible branches of all this.
The thing that it impossible to depict is that intersectionality really creates so many variations of thought that it's never really binary. Both in the religious and the skeptic communities, there are massive internal divisions and disagreements. Richard Dawkins turning out to be a Christian white supremacist is probably not something the skeptic community anticipated and there are certainly skeptics that would disagree with him, even if they overall share the goal of being anti-religion. Of course there are hundreds of versions of the monotheistic religions, let alone the other religions as well, which have been a source of massive strife even now.
I had actually been thinking about this more broadly because of RJC is currently releasing a retrospective on Stargate and as that show went on, it really becomes untenable that they would not use the technology they acquired to help the rest of the humanity or that this US team represented the views of humanity to aliens. They never really went there because, I get it, it's too real to actually sit down and think about how billions of people would react to the existence of aliens and magic technology that could solve all their problems.
I really do think there's probably a really interesting series of novels to be written about this idea and gaming it out, where a global society with thousands of different viewpoints all have to react to some kind of fundamental truth. It's easy when it's alien invaders and you show people with different flags on their military uniforms teaming up to upload virus to an alien computer while the President of the United States leads a squadron of bombers against a massive alien flagship... but what if the aliens were actually Starfleet? And they just want to introduce replicators to end poverty and cure all diseases with a simple vaccine? Would we still kill each other? Would we want to kill them? Thinking about even something as simple as a mask caused so much strife in the last few years, I could only imagine how people would lose their minds if there was actual impactful technology that could change our lives.