It's certainly possible that it is something like that. Let's assume that the dissenters, rightly or wrongly (because it is entirely possible that they erred in their diagnosis), believed that uncontrolled Creation magicks were the issue, or that even the mere existence of this power was a risk. In that case, it wasn't so much that they believed the ancients should cede way to the new life for any supposed moral reasons, but just because they don't possess the same latent potential and thus don't pose the same threat (idk, maybe they thought this would be a "permanent" solution.) So they propose attaching another Primal to Zodiark, or even modifying him, so as to be able to exert some limiting effect on the product of their Creation magicks. You can immediately see why the Convocation might not be keen on this idea; whilst the Bureau of the Architect regulated which concepts could be used (and some Amaurotines thought it was stifling creativity in the process), it would be a different thing entirely to entrust such power - because it is effectively that - to a Primal, and possibly even to Zodiark, even if they revered him for what he did. Meanwhile, if the departed member of the Convocation did not like Primals to begin with (whether they were MIA at the time or not*), one that went a step further and limited their race's main tool in building their great civilisation may have come across as a particularly inelegant solution.
On the other hand, she was unable to do anything like this until you managed to significantly weaken Lahabrea and Igeyorhm, and certainly seemed totally incapable of doing it with Hades (hence the "you have no power over me!" lines if that's what it was about.) She was weaker than Zodiark and I would surmise in her original form, too weak to do anything like this to the ancients. So perhaps the idea wasn't so much to "check" Zodiark but to supplant him with what they perceived to be their superior solution. As an aside, surely they must have also surmised that, with him being in the star itself, the power to sunder would risk fracturing the entire star? Elidibus mentioned the summoners intended to wipe any memory of the ancient world on top of it... still, it may have been unintended.
I also think there is a hint of irony in a Primal created and sustained through creation magicks determining such things to not be "reality". We saw how Ryne ended up when attempting to become the vessel of a Primal - who's to say both Venat and original Elidibus did not end up entertaining similar delusions once they became locked in their war? In the end, with the entire world comprising aether, the products resulting from its manipulation are very much reality, but arrived at through specific configurations of aether. Perhaps the risk with the Primals wasn't so much the tempering, but the fact that they take on a life of their own, although I'll grant they're both rather unusual for Primals, so the jury is still out on that.
*Where I'm going with the MIA thing is that there is the possibility that the 14th took it upon themselves to investigate things a bit more closely within the Underworld itself, which would be a logical place to go looking for any causes of this sound given that it originated there - the dialogue within Anamnesis leaves it vague as to whether they were unavailable, or uninterested, but I hope other language versions might shed some light on it. As for the Underworld, Hades's
short story is interesting in that it suggests it was out of the Ancients' control and something of which they only had glimpses. So one possibility is that the 14th was seeking out a solution to avoid the need for summoning a Primal, but things escalated rapidly, and not only did one end up being summoned, but two, with the world being shattered!