The way I see both of these events is a bit different, I think - but it'll take some rambling to lay it out, lol:
The Ascians seem to be throwing everything at the wall and going with whatever sticks in each dimension. On "The First", they had no chance of doing things the traditional way. The power of Light was inherently high in that dimension and Darkness could never take root; Hydaelyn's chosen made short work of every threat, but then Hydaelyn couldn't hit the brakes. And keep in mind that right before the Warriors of Darkness showed up is in the Post-Ultima phase when She fell silent for a while and ended up too weak to even keep Minfilia manifested and talking. So the Warriors went too far and caused a Flood of Light; the dimension was going to be lost.
Elidibus used Hydaelyn's silence to his advantage, telling the Warriors that they must join forces for the "greater good" and see their world Rejoined, because in this way the aether would live on and they might be reborn through the Lifestream rather than all aether being annihilated by blank, white perfection. But as far as I can tell, if Elidibus's loyalty to Zodiark is absolute (Encyclopedia Eorzea) the the Moon hates the Star's children (Gerun Oracles), this was just pretext. Elidibus didn't give a damn about them or their ability to be reborn one day, he just wanted the aether for Zodiark, and indeed he just shrugged it off when his pawns died. Elidibus deliberately left out that the cosmos was more complex and there were more options than "rejoin or become void", and Urianger exploited that to his benefit.
Elidibus is banking on convincing mortals that the broken universe is an unsustainable, unnatural aberration - an abomination of the cosmos that must be redressed before it causes the collapse of existence as we know it. I have faith that it's more complex than that and just maybe we don't really need to kill entire worlds worth of people "for the greater good".
And as far as I can tell, to Elidibus, Unukalhai was nothing more than another pawn - no different than the Eyes of Nidhogg. Thordan was supposed to eat the Warring Triad, kill all the dragons, and begin a holy crusade to temper the world. Instead he ganked Lahabrea, got ganked by the Warrior of Light, and merely woke the Triad up. The Triad, being unfathomably powerful primals sans the cultures that spawned them, could't be predicted, manipulated, or controlled. They were going to essentially become cats on his chessboard, trampling all over the place and knocking pieces to the floor - upending careful machinations and putting the great war to come in jeopardy (except now he'd need something to take Thordan's place ... say, if the Eorzean Alliance gained more allies and took back two cities).
So he took Unukalhai out of space stasis and threw him at the Warrior of Light. Of course that hopeless sap was going to take in a child with the Echo who never got to fulfill his destiny and lost everything in his world, and of course that kid was going to bond with the allies he never had and end up helping them take the Triad down. And by the end of it Urianger and Unukalhai both don't think Elidibus really did it for the sake of the Light.
Both of these events make him look even more like a villain to me.