The surviving Ancients were morally obligated to free the souls trapped in Zodiark. They had to save their own people.
Sacrificing new souls for that purpose is easily justifiable as they have no obligation to protect those new souls. Would be like a government killing foreigners to save its own citizens. Very basic concept.
If they wanted to go the humanitarian route they could eventually go for some kind of soul rotation. Every x number of years sacrifice new souls so the ones inside can get a break.