Indeed, that's how I see it too. Even with so much unknown, people are still grasping at ways for Zodiark to fit their definition of "evil" (and my take is that I don't think absolutist views make much sense in this respect). Although at this point I am still concerned they'll just reduce it to tempering, which is just another flavour of "zodiark bad", which would be a pity and require overly convenient excuses for Hydaelyn... assuming she did not temper.
A rebuttal would be pointless, because it's true - it's more of a "so what?". His plan is explicitly to re-create the world of the past because they consider it so superior - someone brought up they seem to have no attachment to the ruins; well, yes, it's the world itself they want back. They clearly have no urge to just give up in favour of beings which are not equivalent to lives before the Sundering - his short story even shows a parallel in how he pitied the phoenix he snuffed out, and the mortal lives he's made an attempt to co-exist with but finds fragile and lacking. Up to the point Hythlodaeus recounts, you have the disagreement over whether the sacrificed should have been brought back (because it's only due to them the world even still exists), or should the new life be allowed to continue; that in turn led to the world being shattered. Perfectly understandable disagreement where you can have two sides take a different stance without the other necessarily being "evil". Certainly, from the perspective of the protagonists, the Ascians are an existential threat, and to the latter, the protagonists an obstacle in restoring their world.
Whatever the main point or theme of the story, they wrote it knowing that people would sympathise with one or another character, and that this would vary by personal perspective, as per Oda's comments during the JP fanfest. Possibly because they know it is in the nature of the beast (RPGs) that they will often offer up a choice between sides and perspectives, that their players will be accustomed to such an approach, even if it is not on offer here and whatever main theme there is.
The only real question is how does tempering affect them at this point, because if it strips them of their own motivations, it will all reduce to Zodiark's will/the usual Primal imperative... I still hope SE avoid that route as I'd find it rather lame.
I also wonder if they're going to pick up on the sundered state of the world being a threat to it in and of itself - Oda mentioned this makes it unstable, and it's clear it does even based on what we know, not to mention that it means the Source and its inhabitants are potentially weaker relative to all the other worlds which were not sundered (depending on what base level it started at.) There may be aspects to this we don't yet know, e.g. how it affects the Lifestream, the effect on these worlds of being seemingly hermetically sealed off from the rest of the universe and experiencing different passage of time, Hydaelyn's apparent inability to monitor what's going on within them, and so on.
Same here.
That said, if it's all just down to tempering, I'll lose interest in the whole thing and wait for them to move onto something else. Of course, if they were writing it for such the type of game you mention, they would likely take a different approach, and who knows, maybe the current plotline will ultimately entail the end of not just one but both of the eldest of Primals...