Not all the enemies we fight are killed. Halatali HM isn't a mindless slaughter. Its a Gladiator's arena.
As to the slaughter we do do, it's worth noting that said enemies have other narrative reasons for being seen as enemies. The Kobalds who are mentioned are part of the forces in developing more and more powerful bombs in the Beast Tribe quests. The Kobalds are on a war footing and many of the upper orders are quite oppressive to the lower ones. I did all my Kobald kills doing beast tribe dailies FOR Kobalds. Same for the Amaljaa and the Sahagin. Though in the Amaljaa and the Ixali cases both tribes are actively on a war footing driven by a lust for power and their primal's hunger.
Most dungeons and FATES have a good reason narratively why we are doing them. We aren't just mindlessly slaughtering. We are there to help or protect our allies or stop a villainous plot.
Yes we kill a lot and that shouldn't be ignored. However we don't kill mindlessly or for just a lust for power. Narratively speaking at least. :P
To be honest, I think the thing about the story of the Zodiac Braves that interests me the most is the bit we learn at the very end on why they were called the Zodiac braves.
A reoccurring demon called Zodiac that the Zodiac Braves were each called on to slay and in turn awoke their sentient weapons? Zodiac.... hmm... That name sounds kind of similar to another name in this game... Regardless of any connection, this demon intrigues me.