Sacrifice is never beautiful but sometimes necessary. I'm not arguing that Hydaelyn is some perfect good and honestly I suspect the conflict between Hydaelyn and Zodiark might end up being more of an Us vs Them situation rather than their being some universal good and evil. I will say that from a morality point of view Hydaelyn will probably be the one we are more likely to sympathise with.
I use Nidhogg as an example. Nidhogg is almost certainly very justified in his hatred of Ishgard and humans in general. After first the Allag and then the who Ratatoskr affair his anger is perfectly understandable. However from a moral standpoint you cant stand with Nidhogg because what he wants to do demands a lot of people getting ground to dust. Likewise, the city states are hardly saints but we said with them against Garlemald because Garlemald is the aggressor.
In the Hydaelyn vs Zodiark situation everything points to Zodiark being the aggressor and his minions basically acting without any care to the collateral damage they do. We defend the people of Eorzea as much as we defend Hydaelyn.
As for my comments on Hydaelyn and the lifestream, I go off what we have in game and out of game. Everything we have been feed points at Hydaelyn being not only the source of Aether (All made one) but a benevolent force. More over I again point to the fact that the whole point of the Ascians spreading primal summoning is to drain Hydaelyn of Aether. As Hydaelyn weakens the Aetheric levels around Eorzea have dropped.
I'd also point out that Hydaelyn's nature could very easily be normal in the universe of FF14 (apart from the whole dividing of the Sea into 14 thing). I think Hydaelyn's existence is probably due to that change in the universe. The rules on godhood aren't really clear in FF14 yet. Hell, even the rule on primals aren't. Just cause primals aren't true gods doesn't mean true gods cant exist.
Really we are heavily operating on speculation here. Whatever has happened to Minfilia and her future role could be vastly less drastic than we are assuming. For all we know she has merely become a voice piece for Hydaelyn so she can interact with the world more easily and at less cost to her strength.