The story raises a few questions in sequence.
From what we've seen of Amaurot, they were a secular society. It doesn't look like they viewed their Creations with reverence as 'gods' (as you might expect that in a society of Summoners, instead). Yet when they summoned Zodiark, He immediately became the subject of religious worship overnight. That's a bit unusual to begin with.
Zodiark became the 'Will of the Star'. This sounds like a title of some sort, but it's probably better interpreted in the literal sense. When Hydaelyn became the 'Will of the Star', She was within in the lifestream, merged with the center of the planet. Light is associated with tranquility and stasis, which in turn caused the aether around Her to crystallize into the Mothercrystal.
Zodiark employed the powers of darkness, which as Urianger suggests, is 'the pole aligned with activity and growth'. He stopped the Final Days by accelerating the celestial currents (Coriolis effect?), effectively removing the aether free regions where the Final Days were observed to be initiated from. So if he were to rejuvenate the planet after the Final Days, by becoming the 'Will of the Star', then how would he go about it? I would expect that He would simply accelerate the lifestream from within it to bring new souls to life. Whether these new souls were 'inferior life' worth killing or 'equivalent life' is a bit of rhetorical legerdemain, but let's leave that aside as an unknown for now. Let's hope He didn't have His designs set on eating the West Mandra Empire.
And then there comes the decision itself, as described in 'Ere our Curtain Falls':
'The people were divided, unable to decide what to do with the future that now stretched out before them. Many wished to trade the new life which had sprung forth to reclaim those lost in sacrifice to Zodiark. No small number, however, insisted that the fate of our world should be entrusted to those selfsame freshly minted souls. All were at our wits' end.
At once, we saw it, shimmering. It poured out of Zodiark's breast, and resolved into the shape of a man. As he looked us over─mouths agape, no doubt─he gave what passed for an earnest smile.
"Fear...not... You will make...the right choice. And I will see it through."'
So the people were at an impasse over a fairly significant ethical decision around new souls, which again fits in with the above. And then Zodiark, eldest and most powerful of primals, sends out his Heart in the form of Elidibus, to help the Amaurotines 'make the right choice'. And it's very clear that this 'Elidibus' is nothing like the boy we knew prior to his death.
'I opened my eyes to take in my brother's face, but the lips visible below his mask bore no expression. Would he never again show what he felt for us, as he once had so readily? Were those very sentiments long lost?'
We tend to view Zodiark as a sort of passive agent in all this, because by the time we encounter Him, His Heart is dead, and His body gets treated as a mecha suit by Fandaniel before being discarded. We know that primals have their own will and desires. So what was His take on all this? Why did He seek to influence the Amaurotine decisions around the sacrifices? Did He enthrall His people, as primals are wont to do? If so, this isn't anything new compared to what we've seen with the likes of Ifrit and so on, and we would have been obligated to put an end to Him ourselves regardless.