Well... Doma and Ala Mhigo were both brutally conquered and oppressed territories (former nations); since they obviously did not like Imperial rule, being reviled by the inhabitants of those areas wouldn't make sense. It cannot be stressed enough that the protagonists' actions are purely reactionary / defensive - they are liberators and defenders, not warriors or conquerors. Considering that and the story being told from their perspective, naturally they are going to come across as rather clean.
A few of the Garlean civilians aboard the Prima Vista do offer an alternative view of the Warrior of Light, but a story where they fight on behalf of people who fear and revile them just doesn't seem feasible. You can't save people who don't want to be saved. Furthermore, while we should be infamous in Garlemald... not even every soldier knows who we are despite having made chumps of 3* legates, killed scores of their compatriots, and wrecked countless numbers of their warmachina. Even whose who do know who we are charge us anyway. Against all expectations, I have the feeling the Garlean citizenry... doesn't know who the Warrior of Light is, at least not in enough detail to have them run in terror or throw tomatoes at the sight of them.
*Legacy players get 4 for Nael.
What we individually want from the story is kind of... meaningless, I suppose? We don't write it, so all we can really do is roll with the punches. Stormblood was, yes, a tale of liberation, not war. The Eorzeans have not shown themselves to be particularly interested in making war... after all, they let Ala Mhigo rot for 20 years and only did something about it because they weren't left with much of a choice.