I think the game is positioning Hydaelyn and Zodiark to be almost beyond good and evil. They are summoned entities that perform specific functions - the good and the bad doesn't really come into it.

Zodiark was summoned to restore the world for the Ascians. He was trying to do what he was created for.

Hydaelyn was created to balance him. That is confirmed in the conversation with the Word of the Mother. When he disrupted the balance, she attempted to stop him and thus shattered reality. What we don't know is why Zodiark attempted to disrupt the balance. I think that potentially he went after the aether of the created races and as such she had to retaliate.

Interestingly, if you assume that the number of sacrifices is directly linked to levels of power, then Zodiark should be more powerful that Hydaelyn by many magnitudes. That suggests to me that either Hydaelyn got lucky or those that summoned her had another trick.

I would theorize, that the Ascians that summoned Hydaelyn where the same Ascians that took a notion for creating life. We found out that the Ascians basically created all life on the world. Would it therefore be so hard to assume that in order to protect their creations, those that summoned Hydaelyn gave their lives and also linked their creations to her - giving her increasing power over time? I mean, it would kind of fit. With each rejoining, the population of the Source and the rejoined world is significantly reduced. If Hydaelyn's power is connected to the amount of life on the world, then her power diminishes with each rejoining.