As others in the thread have mentioned, "Light vs Dark" is really "Order vs Chaos" rather than "Good vs Evil". Light represents stability (as a positive spin) and stagnancy (for negative). Darkness represents change (positive) and destruction (negative). Zodiark, the god of the Ascians, is actually an enormously powerful Primal that they summoned out of desperation when their world was literally ending. Enormous change was needed to bring things under control, and so Zodiark is pretty much the epitome of Darkness.
It worked, but was a problematic solution because Zodiark needed a tremendous amount of energy, but for the initial summoning and also to provide him the power he needed to get the job done. Three quarters of the world's population were sacrificed (voluntarily - it was such a utopian society that folks en masse were willing to give up their lives for the sakes of those who would carry on after), and the world was healed and began to flourish with new life. The folks that had summoned Zodiark, though, were not satisfied, and decided to sacrifice this new life to Zodiark in order to resurrect the sacrificed people.
Not everyone agreed with this plan. There were a signficiant number of dissenting individuals who believed that enough blood had been shed, that the world now belonged to the new life. Further, they believed that bringing back the sacrificed would set the stage for the disaster that Zodiark had prevented to resurface again. For the first time in living memory for the members of that utopian society, no amount of debate was enough to reach an agreement, and the dissenters eventually summoned their OWN primal, one much weaker than Zodiark but with a particular power capable of overcoming him: Hydaelyn, who had the power to divide. She divided Zodiark (and the entire world, and all but three of the Ascians) into fourteen pieces, rendering him weak enough to seal away.
Hydaelyn's goal now is to preserve order and stability on the divided world, and to prevent Zodiark from resurfacing. She hasn't been doing the best job - the Ascians decided that the best course of action was to put the world back together again, and they've succeeded seven times so far. Each Calamity merges one of the sundered worlds (the Shards) back into the original world (the Source, where we live), at the cost of extinguishing every life on that planet. The Ascians see this as a mercy - mortals live pitiful, short lives, and are weak in magic, mind, and body. Compared to the Ancients, they barely even qualify as ALIVE. Obviously, as members of this weak, pitful collection of mortals, we disagree, and see the wanton slaughter as monstrous.
So we, representatives of Light, order, and stability, are in conflict with the Ascians, representatives of Darkness, change, and destruction. The Ascians are doing what they see as best for the world, for their lost people, and for quality of life in general. We are doing what we see as best for all the worlds and the people living on them now.
The Ascians DO seem as though they enjoy their role a bit too much, it's true - but there are bits and pieces here and there that hint that they've come a bit unhinged over the millenia, frustrated with the slow progress, the resistance they face, and above all the general AWFULNESS of the mortal beings that now consider themselves to be rulers of the world the Ascians' people once claimed.