Here's the thing, though: while morality is certainly grey, in this war (cold or otherwise) with Garlemald we're the defenders. Garlemald is always the aggressor. If the Garleans laid down their arms and surrendered, there is a high probability Eorzeans (except maybe some Ala Mhigan refugees, understandably) would be willing to let them go home or integrate into Eorzean society. As long as they aren't causing trouble we have no reason to fight Garlemald... it's when they go on the offense that we have to do something. Fighting back in self-defense isn't wrong.

... and yes, us slaughtering Garleans for the purpose of powering up Zodiac Weapons is totes uncool. How canon us doing so is up for debate, though, and the Eorzean city-states do nothing about them.