Endless are not exactly the person they once were. The Sphene we meet is a physical representation of the raw desire to help her people, not the complete human being that she once was. That person is just gone.
Ever played Soma? Gonna spoil the ending:
So, the world is ending and you have to upload the main character's consciousness to the Ark (a virtual world in a ship launched into space) and he succeeds... except what survives is not really him. He copy pastes his mind to the Ark but he dies, and all that survives is his copy, not the person that did the actual upload. Is he truly alive after that? His original self didn't seem to think so, but his copy thought he did, so... who knows.
Anyway, the issue with the Endless is that they specifically require life Aether to exist. This is a problem without a solution that required a choice to be made. Sometimes there's no right choice, only a choice. One is to let Sphene eat every living reflection to keep them existing until all life is gone everywhere else. The other one was to deactivate the memories. Like I said: There's no really a good choice here, but one had to be made, and ending all life in every reflection for the sake of the memories just didn't seem right to me. That doesn't mean I was happy at all to shut down the towers, but a choice had to be made.
The only other solution that I would have tried (if there was an option for it) is to not deactivate the towers but simply let them run out of power eventually by themselves, though I'm not sure if we could have stopped the main terminal (and Sphene) with that method. If possible, that's what I personally would have liked to do.
I believe this whole topic requires a lot of nuance to discuss. It made me think of future AI entities that may become self aware, euthanasia, sacrifice, that one dumb metaphor of the train you have to derail into a city or just a few people (or whatever it was, you know what I'm talking about), etc.
I just hope people remember that all of these concepts are rather complex and that there's hardly one simple definitive answer to all of it.