There was plenty of instances where we were not even given the ability to explain and talk about problems. The lightning-aspected soul sickness for instance... we have a cure for that and we discovered it in The First against light-aspected souls and bring it back to equilibrium. We brought it in the Source to cure the tempering of various races, may it be due to other primal influences like Ifrit, Titan, Leviathan, etc. We have a solution. We never got to explaining it. Plot just jumps ahead and skips it. Why?
Time restrictive setting... it feels more like just poor writing in general.
We have our own set of morals against people who wants to cause destruction and harm, but not all ghosts and spirits deserve to end up getting killed simply due to their racial distinctions. That includes the vast majority of the Endless, who are pretty much harmless civilians other than not knowing their existence runs on Life Aether provided by their original selves. Find a solution for their energy source replacement so the original souls can reincarnate, and suddenly the problems with Sphene needing to kill millions of lives will be solved because there will no longer be a geocidal dilemma. If we just let them be and run out of aether naturally... how much aether was left remaining? Unknown, just pressed for time. How much aether did the lives in Deadwalk Strayborough have the moment they disconnected from Living Memory? Long enough for them to sustain themselves and affect dynamis in such a state where ghostly apparitions transform the entire amusement park. I wouldn't say that's a small amount of time.
The Endless are clearly not a continuation of the original because they lack the soul of the original, but they can exist as an entity who thinks and acts on their own - which is essentially a clone of the original. To kill them means you also see allagan clones also not alive because they are also not the originals. We define our worth in the time we spend living in those moments. Not by the circumstances of our creation. Hence, it does fall more in-line with genocide. To kill or be killed kind of thing.
Sphene may not have figured out an alternative, but that's because she didn't experience what we had to collaborate on one. We have far more experience in esoteric concepts like dynamis and the transfer of souls. Cahciua is aware some lingering Endless who stay in Living Memory even after being cut off from their energy source. They only know it's due to strong lingering emotions -- but that has no explanation to how the lingering emotions make them sustain themselves without access to Life Aether. We couldn't even share the cure to the lightning sickness that plagues Alexandrians. We were not given an chance.
I'm just irked because I would've accepted the result if we could not solve the issue of energy storage after giving our best collaboration at preserving the Endless, but we weren't even attempting to do that. We just ignored the entire situation because the narrative implied clones don't have a right to existence as if we never met clones in the past. To ignore the plight of those one might conceivably save is not wisdom—it is indolence.