It is true that Hydaelyn is a primal. But.

Primals are only dangers if they're summoned / manifested on the material plane; as far as anyone can figure Hydaelyn is not. She's in the aetherial sea where primals go when not manifested, which is why it takes so much energy for her to so much as communicate. Even worse, due to intervening to protect us from Ultima, she's so weakened she needs to use Crystals of Light as batteries to do so.

Hydaelyn is not a permanent solution; at least I don't think she was intended as such. Her purpose is singular: restrain Zodiark by any means necessary. The sentiment behind this is that Zodiark is not a permanent solution to the problem, and that the future should belong to those living in the present rather than those selfsame lives being offered up as sacrifices to bring back those that died in the past. Ideally more research into the sound would have been carried out if not for the Sundering, but either way Zodiark had to be restrained to stop the world from stagnating. (How ironic fate can be.)

It's unclear what caused the sound that caused the Final Days. Popular belief is that it was a consequence of some sort due to creation magicks, but we still have no information on what caused the sound or why.

Hydaelyn is weak because she has no mortal worshipers and no ready source of aether, as well as lending us what strength she can spare to help us defeat the Ascians and unmake their plots.

Despite being a primal, Hydaelyn's raison d'etre is to stop Zodiark from consuming new life to resurrect the dead; to anyone's knowledge she pursues no other agenda, even if the "by any means necessary" clause really means by any means necessary. To anyone's knowledge she is also not on the material plane, thus any aether consumption on her part is unlikely to be a danger. The only reason we'd really have to go against Hydaelyn, based on the information we have now, is if we needed Zodiark off his chains to stop something like the sound coming back... but even that might not be a wise idea considering captive primals are given to rancor when let loose, and like Venat and her followers said it wouldn't really solve the problem.

I don't deny that Hydaelyn's hands are no cleaner than anyone else's, but I earnestly do not see her becoming villainous antagonistic.