Let's jump straight to the thing that caused Faro Plague, biomass conversion. In the ending fight, you can clearly see machines harvest near by biomass to regain more bullets/rockets. While clearly this was for on screen representation, the reality is to really just use the harvest as a mean to get machine functional with energy that they can convert to electricity.(Only new age machine can use blaze canister that could have used combustive engine, but even then it's unlikely.) Let's just say, even a dumb AI can see that you have net loss of energy by trying to convert stable biomass quickly into other forms of fuel that can provide you electricity. I don't care how advanced technology has become in that year, but certainly atomic bond wouldn't change it's nature over time. If machines are either solar(snapmaw) or nuclear(maybe thunderjaw), then they don't need to do biomass conversion in first place, that are cheaper/ready and no need to cause biosphere collapse. Now, let's take it back a bit, it's a glitch and AI don't care. The practical thing is, replication requires resource/energy. You simply requires that amount of metallic materials and energy to even make the machines, judging by the size of corrupter, you probably need about a ton or 2 raw materials. The easiest way to get those is from defeating enemies and acquire their parts and then smelt into replication source materials(again, huge energy loss). It's fairly simple strategy to effectively starve the horus from production of new machines, they will just run themselves dry of any electricity they have and stop production when they run out both energy and materials, even if horus is powered by nuclear, it's not "unlimited" by any means. Remember, they are glitched, so they will not trying to preserve themselves for any long term goal. Simply put, the Faro Plague simply wouldn't be possible, cause our maximum energy gain on earth per day is Sun's radiation energy, and all other loss that eventually turn into background radiation heat loss is gone forever.
Terraforming vs evolution
Evolution doesn't care, you can terraform however you like, evolution simply don't care. Let's say the biosphere is collapsed, GAIA is trying to restore the entire thing back to where human is suitable to live again. The food chain of life means you need to replicate enough machines to kick start the conversion. Whatever bacteria that are left in soil or ocean will evolve and adapt to the environment fairly quickly.(refer to the video how super bug become antibiotic resistant or bacteria just simply evolved to eat plastic around the huge pile of trash floating on Pacific) Whatever environment GAIA is trying to put up, as long as there are some basic form of organism left above the earth crust, GAIA is competing with them, in a sense she need to purposefully extinct those that successfully adapted to the environment and then trying to restore the old ones. Say you restore the nitrogen/oxygen composition of air and other thing so all the species they kept can freely roam around. The moment you release something back into nature, they are competing and achieve their respective balance before you even introduce human into it, although it's a very slow process, but more than likely some of the adapted simple organism will be disruptive and those animals won't stand a chance. And HADES wouldn't even be successfully sterile the entire Earth crust.
AI and centralized system
It's dumb and impractical, even a meteor strike can not eliminate google's data centers around the world all in one go and somehow GAIA is in one place ready to be attacked. As smart as Dr. Sobeck or all the alphas combined, this is easily something they could bring up in early phase of designing GAIA. I don't need to go on and on, it's just alter the practical approach to suit story need, simple as that.
GAIA and cauldron produce machines to restore biosphere and preserve life. Let's leave some of the "later" form of aggressive machines. In the simulation, you can clearly see snapmaw. Now, some of the early machines should and be coded in a way that they will just avoid human(if release into the wild), we have limited supply of human anyway and Earth is a huge place, machines can go other where and continue their work. But no, let's just kill them if they dare to interfere with my sun bath in the river. Or simply walk pass a heard of striker/longhorns/chargers. Remember, GAIA is still in charge before Aloy is born.
You think the people who design GAIA would also tell GAIA to also prevent corruption to happen again when designing new machines, GAIA have years to decode and then send out deactivation code through spire, she could simply also design new machines in a way that they aren't simply overridable and can steadily renew their protocols so even if some old machines are dug up and given new batteries, it wouldn't matter anyway. Aloy's override use the same part from corrupters, so yeah, another bend practical choice to make story happen.
Gut bacteria and machine womb
Early humans from the cradles are fucked pretty much once they are in the wild. Just go search gut bacteria and their relationship with us and food we eat. Machine developed human will have a hard time adapt to external environment because it will be different from what we used to. If GAIA transfer external stuff to develop new gut bacteria culture, our early immune system would and could simply reject them. As gut bacteria relationship is pretty much part of the evolution as well. It might be possible to do some gene alteration to make new humans better adapt to new environment, but alas, the alphas decides to not doing so. Let's just hope one of our reservoir of human genome pool can survive.
Life vs Knowledge and confusing role of GAIA
To preserve life, humans are not required, as we could destroy the biosphere. To let humans keep going, preserving knowledge to avoid repeating our destructive nature is much more important. AIs could have just say fuck it and developed android that are powered by disconnected cyborgs that are part organic and part mechanic. Like GAIA reflecting it's thought of multiple mass extinctions, I wonder if she feel that the reason she feel what she think she does, simply because the conscious part of herself are embed with knowledge and value from the team. So essentially, the wasted cycles doing the feelings, are what makes human human. And, human aren't really required to keep those intact. It is simply another stage of evolution, homo sapien ends here, GAIA can do whatever she like to do in the future.
Corrosive nature vs waking up the old swarm
And last but not least, our earth crust is very very corrosive. If you see how shits gets breakdown in nature, HADES are in for a big surprise when it sends out the activation code and no one would've responded. The HZD timeline shows that between swarm gets deactivated to HZD begin is around 1000 years. Helis couldn't dig up something even remotely usable and probably would just destroy HADES for good. Even the seal environments are pretty much broken everywhere already. Even cauldrons.
Here you go, I'm not the smartest kid in the block, feel free to discuss and pointing out where I'm wrong.
edit: formatting and some typo, I might have more but please forgive me.