Thing is - New Eden is neither a natural, nor a stable society.
By all accounts, this current society is doomed to die out anyway - currently they live in a post-nuclear age society, still leeching off from the stuff brought back from Earth. Their current religious rule only works as a transitional rule - if the population grows, they'll have to form completely new, different ways of organizing themselves. They lack modern factories, fabric, materials they all have currently in use - I didn't saw any coal or iron mines, nor domesticated animals. They'd pretty soon degrade to a stone-age era society witout artificial help. And if they continue to live off from their 21st century knowledge - that doesn't count as an "own" society either. All of that completely ignoring things like genetic diversity.
Like the Ba'Ku - the Prime Directive doesn't apply in this case. But that doesn't mean you can just haul them off the planet carelessly either.
Personally, I would advocate for carefully re-establishing contact wit humanity - and then re-settle them to a human colony planet, where they could individually decide to leave "New" New Eden, or stay in their society, but now contact to the rest of Earth.
That being said - this is probably something that needs to be done in a few hundred years in the future, considering how far they are away (and only the Discovery with the spore drive can reach them) - and if, by that time, they truly have forgotten Earth and reverted to a middle-age society, the situation would be completely different again.
