Hydaelyn's purpose was to "bind" and "hold [Zodiark] in check" - even Emet-Selch never goes so far as to say the Sundering was a deliberate, premeditated action on the part of Hydaelyn or her summoners. Of course, binding their savior would be sure to piss off Zodiark's adherents - especially the tempered Convocation - but the intent of anything other than binding him is purely speculation.

Azem bits:

1. The PC is not literally Azem of Amaurot. They are Azem reborn in the modern age, and their own person - not bound by whatever the last Azem of Amaurot did. "It's strange / improper for the PC to take sides because Azem didn't take sides" doesn't make any sense.
2. While Azem refused to participate in the summoning of either Zodiark or Hydaelyn, once that die was cast they might not have had a choice one way or another. They were a champion and hero to people the world over, not just Amaurot. What difference would it make, though? (See 1 above.)

Meanwhile I'm lookin' at the Pandaemonium description and thinkin' to myself, "Yep, there is totally no way at all the Ancients could have been responsible, knowingly or otherwise, for the Final Days and their fall from grace. How could they be, Emet-Selch said their society was perfect and lasted forever beforehand... nothing could possibly have gone wrong."