I'm about as "Team Hydaelyn" as it gets, but I'll try to keep my bias in check here, lol.
Yes; in some ways more than others, She can be thought of as less-than-implicitly-trustworthy. She is one of two diametrically opposed extremes that seems to have resulted from the will(s) of the aetherial sea drifting apart. When either of these wills interfere with the world, the balance is tipped. When the balance tips too far, nothing good can come of it—even if the Light is the victor.
A summary for the sake of establishing my point of view:If the story we've been told is accurate, Zodiark was the first to threaten the balance—by taking too much power and threatening Hydaelyn. By expelling Him to/as the moon, she robbed Him of His power to influence the world(s) and His place in the sea. Incidentally, this stress on the cosmos shattered it into the original world and thirteen copies of it.
Since this time, He has been using the Ascians to exert His influence, destabilizing worlds with Chaos and Darkness in order to weaken the boundaries that exist between them in order to Rejoin the shattered pieces and resurrect Himself with their aether.
Elidibus keeps the Ascians from going too far. The black-robed Ascians are blinded by their lust for power and Zodiark's favor to the point that they will undermine one another and let an entire world be lost to a Flood of Darkness (which will create a void that Zodiark cannot use to empower Himself).
Until recently, Hydaelyn had no such emissary, which meant that Her own champions could pull an Ascian move and zealously keep on tilting things towards Light unchecked—believing they were doing the right thing—until the Flood destroyed them all. I'm surprised it took this long for The First to happen (unless She'd previously held back for this very reason but could no longer take the risk having lost this much).
So yes, Her efforts for self-preservation and the protection of Her children are less than measured, and in that sense we can't rely on her implicitly. Now, do the ends justify the means? We've been led to assume so. We've been led to assume that a world dominated by Zodiark would have no place for mortals at all. A world where mortals are "merely" at risk and continually struggling seems preferable for the time being.
The reason I keep faith with Her is because all of Her actions have been as far as we know reactionary. If Zodiark didn't threaten the balance, if Zodiark didn't send the Ascians, if the Ascians weren't threatening the existence of entire dimensions, She seems perfectly content to sit in sea and do nothing. During the Astral Eras, when the Dark sat idly by and let the world recover to the point that it could be coerced into throwing itself into chaos on a level required for Calamity once more, She did nothing but let Her children thrive.
At this point, there's just too much suggesting that She's the only one who'd have our backs in a fight, the only one who'd sit by and let Her children control the reins of history in their (as I've grown to refer to it) beautifully broken and balanced cosmos.
However, anything could upend this point of view. There's much we haven't seen.
From this point on is a tangential digression.
I'm hoping that Elidibus is the true bad guy here. He is the closest thing to Zodiark's actual will that we have, and he is a master of manipulating your point of view so he seems reasonable and justified and not a threat to your greatest interests. However, he does this not only by providing information that confirms it, but withholding information to the contrary. If we had nothing to fear on the greatest scales, he wouldn't be hiding his greater ambitions on the tiers just below them, in my humble opinion.
Also imho, in order to keep the story interesting until the end, Zodiark either has to be more than we've been led to believe, or He has to be undermined. It would be interesting to see that Zodiark simply has a different point of view about how life should manifest, given that he is associated with soul just as much as Hydaelyn is associated with the planet ("the star"). In this case, Elidibus would be finally vindicated in his assertion that he just wants to put things back how they were—the Sea would be rejoined, the world would be made whole, the binary would be brought back to center, the war would end. However, every time Elidibus speaks of this, there's a slyness about it that I don't trust at all. He didn't even pretend that mortals would make it through this transition back to the cosmos's original form, and that's just for starters.
Therefore, I'd prefer that Zodiark truly was everything we've been led to believe (though perhaps they could make us falsely doubt our instincts on that and question whether the above were the "right" thing to do). What I'd like to see is Elidibus come to terms with that. I'd like to see Elidibus realize that Zodiark is an active threat equal to Hydaelyn's reactionary threat and give himself wholly over to the Dark's lust for control and determination by usurping the entire plan. I'd like to see Elidibus attempt to rejoin all of the worlds, destroy everything that is, including both crystals, and reboot the entire cosmos as a healthy, newborn Genesis in his own image. Who could blame him? ... But for the sake of everything we are and everything we've fought for, he'd have to be stopped.
This would fulfill both Final Fantasy XIV's desire to on the deepest level be Good versus Evil, Light versus Darkness like the classic Final Fantasy titles, without being so simple. It also allows XIV to continue the ambiguity whereby Light = Good / Darkness = Evil is incidental. Hydaelyn just happens to be the one with our backs, not because Light is Good. Some past titles, as well, have had the truest evils be neither inherently light or dark.