You said philosophically, so I'm shooting entirely past any in-universe material divisions here like the presence (or lack thereof) of a soul here. Which is good, because I don't think that argument matters.
Essentially, the core difference in reaction to both of them are actually in exactly 'how they are sustained'. Both were essentially recreations of people, but their root reasons for existing and cost are different. Ultima Thule's people, including the people we met in the Omicron society quest, essentially do not have a meaningful 'cost'--either whatever they're running on literally can exist perpetually, or the question of what they're running on just wasn't especially relevant to anyone we talked to. The Endless, on the other hand, have a very concrete cost: corporeal aether (a.k.a. life force, different from souls; not the most clearly stated thing), harvested from living people, preferably yours.
There's also a question of why they were made in both cases. Ultima Thule's denizens are, in a weird, twisted way, created for their own sake: Meteion made the originals essentially to make them suffer, and then the Omicrons later made some simulations for the purposes of giving them whatever form of closure and community they can. They are there for themselves. That is actually not true for the Endless: they essentially exist for the sake of the living. The Endless are a twisted manifestation of Alexandria's belief that you live as long as you're remembered; they are, essentially, an extremely elaborate photo album of the deceased. ...but a photo album is only worth having if you look at it, so you have the deep, tragic irony that because of the regulators' memory erasure, nobody is looking at it. Compound that with the exorbitant cost required to keep them 'alive'? We can only ever pull out the blade against that.
If the Endless weren't running on literal human lives, we'd probably be cool with it; we actually didn't really shut them down due to an objection to the Endless, we shut them down because they were the thing Sphene was willing to kill entire planets for. But they are a memorial to the dead; the worst thing you could do is keep sacrificing living people to it.



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