At the end of the day, any argument that you offer up to justify Amaurot's decision start sacrificing non-Amaurotian souls to Zodiark will hinge on the belief that those living individuals have less value than a bunch of dead Amaurotian souls. Which is very similar to Emet's reasoning when he slaughtered the people of seven worlds to have his rejoinings. He justifies it as not being murder because those races, those people, are somehow less than human in his eyes. And it's incredibly hard not to see the problem with that.

I don't see why that last set of sacrifices needed to happen, either. If releasing the souls was all that important, then just destroy Zodiark to release them. That is, if the Amaurotians truly believed that they had solved the problem. If they genuinely planned on keeping Zodiark around forever, then it shows that they willfully ignored the problem.