As soon as soul transferring stuff is mentioned, Alisaie hates it. Wuk Lamat outright tells Sphene they should stop it (what happened to respecting others cultures and learning first?).
But thinking about it... The soul is extracted, wiped clean (which the game itself says is done in the aetherial sea too), and then popped into a regulator to save someone from death. When used I assume it then goes to the aetherial sea where it goes back into the normal cycle. So at most, you're simply delaying the rebirth of that soul for a little bit and giving the person who used it a bit longer.
Ignoring the souls they forcefully take (because when we're first told we 'don't know' that they're forcefully taking any as despite having seen it none of the characters are smart enough to put two and two together). The souls taken from their own citizens are voluntarily given. How is this different from someone giving blood to save anothers life? Or as giving blood doesn't kill you, how is this different from organ donation of say a heart from someone who died going to a person who needs it?
(For that matter, how do they have enough spare souls for everyone? If at the start they all had one extra soul each half of the population would need to have died... Let alone having more than one soul each which is implied by the fact that they can buy them. Did we skip the part of their history where they harvested the souls of all their neighbours? And they have such a shortage yet accepted the people who got stuck in the dome into their population instead of just harvesting them, that means they would have been using even more.
Also, if the Endless are just electronic versions of a souls memory, why do they need souls to power them? They're not alive, all they should need is electricity/power, not souls (if they need souls, that means they are alive in some way). Seems to make far more sense to me that they would need all the souls to keep their living population supplied as that seems like the most unsustainable part.
I'm also confused about the passage of time... Supposedly a few days passed from the dome popping up to us going in. This was 30 years inside the dome, so let's say 10 years per day. Otis says he's 400+ years old, which at a day per 10 years would be 40 days since presumably Sphene first died and the dome went up. Or just over a month ago on the source. But Kriles parents left her behind 20 years ago on the source which would be..... A very long time ago on the shard.)