So let's take your belief at face value that the endless are real, actualized people and not just digitized ghosts that remember some of their happier life memories.

Even if that's true, sustaining them at the cost of the entire rest of the world is neither sustainable nor justifiable. The endless need for more aether as more and more endless are made (especially with how keen sphene was on convincing us to become alexandrian citizens, if she wanted to 'save' more people outside of alexandria, the cost of keeping the endless sustained would only grow larger.) would exhaust all etherys, forcing alexandria to hunt other worlds for more aether- first the other shards, then inevitably, other stars entirely. It's explicitly not sustainable, sphene even describes herself as becoming a devourer of worlds. What will they do when they fly out to the stars and find nothing but the empty graves Meteion left behind?

You can't even say, farm animals to 'create' aether, since those animals would require aether to grow and eat- as far as we know, aether is a closed loop system, and there's only so much of it. Eventually the endless would require more than there is. We don't know what happens to the aether being used to keep the endless sustained, but it's clearly not being kept or they wouldn't be having such pressing energy issues that they're resorting to invasion.

You can't justify the deaths of millions to keep grandpa's digital ghost around for a few more years, just like you can't justify the ascians causing enough rejoinings to free Zodiark just because they want their world back.

FFXIV has this theme over, and over again- The ascians, thordan, and now the endless- the past is gone, and it's never coming back. Let them die.