With the exception of Azem, (for a reason we do not know) next to no one disagreed with summoning Zodiark. Not even Venat discounts the fact that using him was essentially the only thing that the Ancients could do to survive, and continued to be the only reason people were surviving for the next 12,000 years. Elidibus made that choice and took that burden when the Ancients as a people had unanimously decided upon that course, before conflicts had ever arisen in the first place. There was nothing to 'agree' with, it was just the right thing to do. I fail to see how taking up the mantle of Zodiark when he was inarguably their only option belies some inherent bias on his part. I also don't think looking at Elidibus the way he is when their circumstances are completely different several millennia later helps to gleam how he would have acted then.
I also take issue with the placement of Elidibus's emergence from Zodiark being this early on in the timeline, as is being speculated here. The novella offers no further clarity on that front than what we already had. Again, Emet-selch was not talking of specifically the Convocation in that passage, or if he was, it isn't made clear, so we can't know if when the Anamnesis scene occurred, Elidibus was even there yet or not. If it is the Convocation, why is there apprehension towards Zodiark in the first place? I thought they were tempered when he was summoned? In that case, why did Elidibus need to withdraw himself at all? Either the tempering doesn't matter, or this is not referring to only the Convocation. Or maybe they were tempered but only a little bit because their souls are so massive they're resistant, so they kind of but not really have their own will?
See there are just too many unknown variables to come to a conclusion anyone will be even halfway satisfied with. Zodiark's tempering, the proper timeline of events; we are left in the dark on all of it, when we really should not have been. I get leaving some things to the imagination, but at this point we are making entire headcanon scenarios out of the tiniest scraps. I don't think this avenue is really gonna lead anywhere.