The Warrior of Light is a warrior and adventurer. By the nature of being a warrior, people are going to die. The world of FF14 is an extremely violent place.
There isn't an easy way to justify things in any violent setting in a moral way. We end up killing a lot of peoples only because they held a different viewpoint or goal to us and were unwilling or unable to see an alternative option. The Garlean soldiers are a perfect example. A lot of them are conscripts who never wanted to be there in the first place but there is no way around freeing Ala Mhigo than fighting them. Even is some were open to turning on Garlemald, the Garlean policy of taking retribution on family members of traitors would stop that from happening. So what does the WoL do? Just give up?
In FF14 there are often not truly villainous sides. Many of the enemies we fight, we do so out of a difference of ideologies or because the lengths they are willing to go to put the lives of innocents at risk. It is ironic that in the SAM quests you actually fight against revolutionaries seeking to bring down corruption in Hingashi because their method requires anarchy and war which would see thousands of innocent people die in power struggles. The cause is just but because of the method and the cost you are forced to cut these people down. If you didn't thousands would die.
That is the reality of morality. It is often not clear cut, particularly when things get complicated. The WoL can just try there best and keep fighting in a war that often seems impossible to win. The point is that the WoL tries anyway. I think in the end this is part of the reason why we will end up aiding Garlemald at some point. After all, they are Hydaelyn's children too.