I don't even think "moral relativism" is the right term here, even though he used it - it's more that they don't consider most life forms following the Sundering to be relevant to moral considerations at all. It's a two step thing - 1) they poured in a great deal of sacrifice to get their world back up and running and 2) they had intended for Zodiark to cede some power, after the world was nurtured, and restore those who were sacrificed. To then have half the aether of the world consumed and have it sundered, resulting in beings nigh unrecognisable to them, it becomes clearer that there is absolutely no reason why they would see anything coming thereafter as legitimate forms of existence. This applies even if they did not intend to restore the sacrificed, since by all accounts, those who gave themselves unto Zodiark to restore the world did so freely and this was down to the nature of the original race, something Emet-Selch himself brings up. They want things restored as to how they were and were not responsible for the Sundering.
Now had Emet-Selch, the Convocation and those who sacrificed to summon Zodiark themselves been responsible for Hydaelyn and what followed, then there's more of a case as to why their viewpoint would be illogical or hypocritical - but they were not. On their view, to restore life to how it was all the aether broken up across woulds would have to be re-assembled. Thus, he thinks the potential of such post-Sundering lifeforms is inherently stunted. Also, whilst the Ascians stir the pot, let's not pretend there wouldn't be conflicts without them. They merely engineer their scale and exploit existing opportunities. It is precisely this perceived imperfection in man that they are utilising to realise their ends. By all accounts, their race did not necessarily lack similar impulses but had learnt to transcend and manage them. They don't think the sundered lifeforms even have it in them to get to that point, where 75% of the race would condone to sacrificing itself to save its world, cleaning up whatever mess plagued it.
Moreover, it is revealed in the end that you are one of them; no less, in all probability, the member who left the Convocation, thus why you can contend with them, albeit in Emet-Selch's case with a lot of help and circumstantial advantages (i.e. the built up corrupted Light.) That really doesn't serve to do much to undermine his case.
The fact that some of Emet-Selch's own people summoned Hydaelyn does not mean he would not loathe the culprits for it and for undoing the plans they had to restore those sacrificed, and also for shattering their race and their world. Sure, it is a contest of wills, but his scorn for diluted life forms as he sees them does not mean he cannot disagree over the actions some of his own kind took or that he thinks those of his own race cannot err - after all, they were no hivemind. Yet what material difference does it make to them and where they find themselves? That isn't to say that I think it means our characters should just take it lying down - clearly not. It just moves the issue for me to an area where it boils down to irreconcilable differences on fundamental premises of morality between the two sides, rather than dealing with a pure villain like Zenos.
That said, I am sure, given how the story is being written, that some element will be thrown in to show how it was "necessary", i.e. some plotline that the Convocation members became corrupted, and/or altered their plans, rather than going down the more interesting route that both gods were ultimately mistakes. I'm also fairly confident that they'll have you be the departed member of the Convocation, who rallied others to her summoning. Perhaps to cease the sacrifice, perhaps for other reasons (Zodiark spiralling out of control, for example), though the method in question does make me think it would be more than just the sacrifice being made to Zodiark, or maybe the reasons behind it, but if no end seemed in sight, then mayhap it was that. Not the route I'd like them to take but it seems plausible and it would alter matters in terms of the logic behind it.
Regarding the effects her excision would have - the planet could certainly survive without her, although quite what those "Terminus" monstrosities truly are is unclear. Going from the NPC dialogue in Amaurot, the affair was described as a screeching cacophony beneath the earth, distorting living things and wresting from the ancients their creation magicks - this then ties in with Emet-Selch's voice during the dungeon, in describing how their worst impulses, their sins, were given life through the power of their creation magicks. They could not point to the source and even through Emet-Selch's recollection, it does not seem to have been determined. To me, this all is indicative of some manner of parasite, possibly even an otherworldly one, but nonetheless something within the planet which caused this suffering. I'd also leave open the possibility that in some places outwith Amaurot, they may have been less diligent in self-regulating their powers of creation, but by the account given, parasitic activity sounds likely.
Whatever their origin, in that event perhaps having such a "will in the star" could be beneficial, to ward off the possibility of such an event recurring. The other big question is how would life on it alter? Certainly, the natural environmental aether and things like forests and such can clearly exist without a planetary will. It's possible that the world would change somehow but to me it looks like all that aether is contained in the Primal itself, and its release would just mean an awful lot of aether to be harnessed. Unless they're somehow conducive to naturally balancing the world, to avoid calamities like that which befell Amaurot, or for some other reason (i.e. the fragmented life forms since the Sundering somehow depend on them to exist), their existence at the least appears to be negotiable. So I'll agree that we need more information to see what to make of all this, before concluding that their excision is 1) feasible and 2) desirable.
Lastly, I wonder whether the persistence of the alternative 8th Umbral Calamity timeline G'raha postulated as a potential scenario (implied by his own persistence after it is forestalled) may mean a possible way for the Ascians to summon Zodiark without rejoining the Shards in this timeline, were they able to exploit this. It'd enter very messy territory in terms of the logical implications of such a state of affairs, but it's a viable avenue if SE wanted to leave the other Shards untouched in our timeline but have Zodiark summoned.
For full disclosure, though, if this were a game where we got to pick sides, I'd side with the Ascians.Their reclamation narrative and alignment to darkness greatly appeal to me from an RP/fantasy perspective.