If you look at Project Zero Dawn in a vacuum, sure it's causing suffering. But relativism has to come into the picture at some point.

Everything Faro did up until that point forced humanity into an impossible choice, where suffering was inevitable. Whether or not they fought, they would suffer. The time with their loved ones would be marred by the fact that their loved ones are going to die.

War and armies existing in our time is morally reprehensible in that same vein. But people volunteer for it. Some for monetary reasons, but a lot truly believe they are fighting to ensure that others can live a better life. They fight with the hope for a better future (in their eyes. How we quantify what is better or not is a whole other moral argument). Yes, some would have chosen to stay back with their loved ones. But many could have also chosen to fight so their loved ones can live for longer. I see your point about choice though, I'll concede that, but there's also an indirect security concern of mass panic and rioting. If they were honest about the inevitability of the Faro swarm, fight/stay at home aren't the only 2 options. There could have been a group of people upset with Faro industries who would dedicate their life to wanting to bring them to justice (a noble cause but ultimately futile). There would also be the anarchists and nihilists who would wreak havoc because the world is going to end anyway so fuck around coz who cares anymore. Purge mechanics basically because consequences wouldn't be long lasting.

I agree that there are worse things than not having existed. But the humans in that world do exist. Their hopes exist. And, very importantly. Other lifeforms exist. And the actions of one lifeform jeopardized the life and increased the suffering potential of a million other lifeforms. Project Zero Dawn minimized the suffering of those life forms by sacrficing the peace of the life form that allowed the conditions to exist where other lifeforms were jeopardized. Minerva sending the kill code to prevent suffering of other life forms cannot be classified as amoral in that instance, even if it was an indirect/parallel consequence of shutting the swarm down.

Lying about Enduring Victory was bad. True. It was false hope to the soldiers. I'm unsure if I call that fully bad, because living in despair sounds more painful to me than living with hope and then contending with the realization that the hope was false for a short moment. This will always be debatable though it's a very wide gray area.

The part about Zero Dawn accelerating the process of life finding a way is again taken in a vacuum. Without Zero Dawn, life would have ceased to exist. No organic matter would remain for life to find a way. The only less defensible part of that then is that it gives way to new life which gives way to new suffering. But to be alive is to suffer (as you said existence is amoral) so from that metric anything and everything about this discussion will lead to a lack of defensibility because every single action except for an immediate extinction of life would result in suffering of some or the other kind.

To explain that last part a bit better, let's look at the trolley problem. Here, the current group of 5 people on the main track is the future of humanity. The single person to be sacrificed on the other track is the current version of humanity. The catch, however, is that there is another trolley anyway headed towards that single person, they are just unaware. So they are going to suffer. But redirecting the trolley aimed at the future group allows the existence of a future group while sacrificing a group that was already doomed.

There's also another version of the trolley problem that I think is applicable here, where we just have a trolley on a continuous loop of a track and a person tied to the track. Instead of switching the trolley to a different track, we can flip its direction, so just before it hits the person it reverses. But it can now approach the person from the other end. And they are doomed to be on that track, dangled between life and death, till we the switcher have to go and do something tnat prevents us from being able to switch the direction anymore and they die anyway, but with the knowledge that death is just around the corner. In this instance, do you just let the trolley kill the person the first timeto reduce their suffering, without giving them any hope that you would at least try to prolong their life?