The sooner people detach "light and darkness" from "good and evil" the more this debate can progress. The two pairs are unrelated.
You speak of "sides" but that's the kind of view that gets hundreds if not thousands of those bystanders slaughtered. That said.
https://youtu.be/A4ogo3d8Fp0?t=52m37s
"The sons must pay for their fathers' misdeeds. Only then will the cycle be broken" - implies she wants the war to end and thinks Ishgard is in the wrong but that's the absolute mindset of a murderous tyrant.
"The sinners' feeble magicks are undone! Come! Claim your retribution!" - she knows this is all about revenge, she knows what's about to happen.
But see here's the thing. What ambiguoity you had about her here goes to hell with this:
"Ahahahahahahaha!"
This is not someone good. This is a crazy, bloodthirsty murderer who just unleashed beings of untold might and magicks onto a city that not all of them are capable of even fending for themselves. 3.0 retconned her character, and retconned her hard, but this scene clearly paints her as a villain. She's not just an antagonist, and we've seen our fair share of people who stood against us but were in it for the right reasons at lesat. Ysayle, as depicted in 2.5, is just bad.
You want someone who knows the wrongs done and wants to fix it? Aymeric. Hauchy. The WoL. Ysayle snapped out of it in 3.0 but that doesn't erase her actions in 2.5, and in many ways, the only possible conclusion to her story after that was a redeemer's death.