Light destroying every living thing is almost a direct quote from 3.4 about what happens with a Flood of Light. Which the Ascians wanted to happen and Hydalyen didn't want to happen. But ever since Lahabrea set Ultima off, she's had a very, very hard time marshaling enough strength to get through to the Echo-users.
One of the biggest "what-if" scenarios for FFXIV I've thought of is "What if Ultima never went off?". Everything we've seen about Hydalyen suggests that if she had the strength to talk to Us, Ysayle and the Warriors of Darkness she would have. All throughout 2.0 she's directing us to stop the people who are trying to destroy life as we know it so that Zodiark can come back. And then when the super-powerfull spell that would have killed us goes off, she saves us at great cost to herself because she loves life and can't bear us dying.
People turning out to not be who they say they are only works if that reveal has some foreshadowing. I can't think of anything Hydalyen has done that could be foreshadowing for her not being the Big Good of the FFXIV world. Her weaknesses seem to stem not from her wanting to be weak, but the machinations of the Ascians making her so weak she can't act. Given all the times she has acted (giving us crystals of light, saving us from Ultima, giving us the aetheric energy needed to expel Lahabrea from Thancred, pulling back the light from the First Shard so it isn't overrun with Light) people have been saved who otherwise would not have, I can't seen any foreshadowing for her wanting something different. When you can trace most (if not all) of the sources of Hydalyen's weaknesses back to the Ascians who want her to be weak in the first place... That feels a lot more like proper foreshadowing.
The other thing is the "springing" the surprise that Hydalyen has been bad all along goes directly against what Yoshida has said about what he thinks good and bad player speculation is. And how he wants to included hints that lead towards speculation that turns out to be correct. (Example: drawing attention to a certain person's mask because the player base will recognize it and think it is the person it really is vs not being clear enough about Zenos possessing someone random as opposed to someone who looks like Harchefaunt which causes people to incorrectly speculate it is Harchefaunt's body he is possessing). I'd think if they were going to do something this huge, we would have seen in coming long ago instead of only "seeing" it coming if we assume nearly everything in the entire game has been lying up to this point about what Hydalyen is. Except the people who are known for lying about their motives for just about everything they do...
There's also the larger context of the Final Fantasy games to consider. Ever since FFX, the plot of the single-player FF games has boiled down to humanity vs the gods. With the gods always having non-benign motives for what they do. After a while, that gets really old. And for all the FFXIV takes ideas and plots from other FF games, it usually puts it's own spin on them. Seeing it subvert the "gods do not have humanities best interests at heart" plot would be a breath of fresh air.