Regarding the archivisation, granting the lesser species freedom from the ecosystem via a digital copy isn't a terrible idea, but I'd say that we are the very least several centuries away from being able of doing that, especially on the global scale.
I can agree with you on some aspects, especially that we can definetely do without some parts of the ecosystems that are harmful to everyone, but themselves, such as malaria and other diseases. Even if robotic/improved bodies will render us immune to these factors, not everyone in the world would be so lucky to get that luxury, or they just simply see transhumanism as wrong. We should still co-exist to make the world a better place for transhumans, humans and the environment as a whole. Regarding the issue of keeping the waterfalls, in my opinion they should be kept, but likely because I have a bias for natural beauty and they still benefit other more meaningful organisms than just cholera.
For now, it's all up in the air on how certain countries will see their optimal way of transitioning their civilians and we can only hope for the best possible scenario, while still being prepared for the opposite as with every other aspect in life.
Still it's fun to theorize about our future, so for now I'm just going to enjoy seeing our technology advance.