Thy Life is a riddle, to bear rapture and sorrowThis is just one place we differently exercise our interpretive inclinations.
To listen, to suffer, to entrust unto tomorrow
In one fleeting moment, from the Land doth life flow
Yet in one fleeting moment, for anew it doth grow
In the same fleeting moment thou must live, die and know
Keep in mind that I can't detach my experiences in 1.0 from my assessment here; it inevitably colors my evaluation. Those experiences make it a lot more likely that to read into the story the implication that if you hear, "Hear, Feel, Think" and your response is "No, thank you." That's fine. You don't have to join Her cause. You don't have to listen to Her. Plenty of people walked away, ignored it, or never even realized they had it. Some fought with Her enemies. You can choose to never tell anyone you have the Echo and use it solely to cheat at poker and you'll face no consequences. You can attempt to axe Her emissary in the face and She'll still call you Her beloved child.
Regardless of what or who your soul once was, you were born into this world. You were given this choice. And, unfortunately for the preferences of some, as the protagonist of this game, you fight for Eorzea as it is. Not as it was 12,000 years ago, not as it could have been, but as it is today and the the best it could be tomorrow. We fight for the Scions, and the Alliance leaders, and everyone with the willingness to be those who walk before to lead those who walk after, and (so far) She validates that constantly; we can't help that part, lol.
I'm just doubful Naoki Yoshida intended that journey to be interpreted as "you spent 10 years being the suckered slave of a duplicitous false god" when in the midst of the greatest chance he had to set that narrative up, Shadowbringers, he didn't even let you wield Darkness yourself (even after it was the entire theme of the trailer) when it was the only thing that'd beat the Light. He had you use Hydaelyn's gift to absorb and negate the Light and then use it against Darkness. In the words of the wise Excalibeard, "The dude wouldn't let us play thief." What are the chances that guy's intended reading of the story is "Screw the Mothercrystal"?
It doesn't mean she's perfectly benevolent and has never made mistakes.
But summoned entities believe they are what they were summoned to be. She was summoned to see the new life as her precious children to protect forevermore. Did Hydaelyn lie to you any more than Ifrit or Garuda did when they acted as though the only narrative summoned into them was the Truth? And if we take into account that Hydaelyn's narrative might be flawed because of what She was meant to be, what of Zodiark?
In short: If Venat's position was "The planet belongs to life newly born, Zodiark is a threat." then Hydaelyn (probably, as far as we know) inherently sees you as "Her child" and is in your corner. And that is biased - I've been spraying #TeamHydaelyn tags on walls for years, lol.
I'm not even 100% confident She'll survive 6.0, I just don't expect to loathe Her.