I like the idea that Hydaelyn is a fake, or stand-in, for Zodiark, and I agree that her status as a stand-in does not necessarily mean she's "evil." That being said, lore wise I'm not sure I'm as open to the idea that she is some form of Primal.
I've been taking most of my lore ques on this subject from the previous games that SE seems to be drawing content/inspiration from. So, if SE is holding strong to the lore of FFVI and XII/Tactics, it stands that there are "Gods" that are absolutely not dependent on Human prayer/faith/belief to sustain themselves and may, in fact, be the source of aether rather than requiring it to survive. The biggest nod to this is the recent addition of the Warring Triad to the game. If SE keeps the lore in tact, than the Warring Triad are not Pirmals/Eikons, but rather they actually created the first Primals in order to war against one another. If Hydaelyn and Zodiark are above them than I highly doubt they're Primals (albeit very strong ones).
Honestly, SE could just be making this all up from scratch and recycling the names from previous games (wouldn't be the first time. See Cid's numerous incarnations), but I really hope they're not. I think I'd find the original history to the Warring Triad much more interesting in the context of FFXIV than simply having every new "god" we encounter be exactly the same and have the same fundamental nature. For one, it would be boring to think that the most supreme and elite of all the gods/superbeings in FFXIV's universe are going to be explained as: "oh, it's just a really really strong primal," and it just wouldn't make sense, really. I mean, in theory. At least some of these deities have to have existed before humanoid species evolved. They can't be sustaining themselves on our faith if we didn't exist at the time, right?
Also, if all of the gods, Hydaelyn included, turn out to be primals, than the logical solution to all of the problems of FFXIV would be to simply put a stop to belief entirely... Which would probably require the mass genocide of all species, everywhere, throughout the cosmos... Admittedly, that would make for a very interesting plot twist, but I don't think we've seen any villains in FFXIV so far who have that kind of special brand of Kefka level insanity.