Broken window fallacy.
War tends to advance scientific research into militarily useful fields, that eventually get expanded into civilian uses in peacetime; the example that gets brought up is GPS. However, this also tends to freeze research into more blue-sky goals, like curing cancer or eradicating smallpox. This is also not including the damage war does to infrastructure, including that necessary for research.
In FFXIV, we've already seen one example of peace causing stagnation, viz the Allagan Empire. However, their wartime innovations cannot be said to be wholly beneficial (obviously), and we do know that Xande's attempts to speed up progress by executing one member of his research staff every day until they produced results is probably not the most efficient way of enhancing scientific research in all areas.
Overall, it is usually unquestioned that war brings with it much evil, regardless of the intent or justification. The debate is whether it is a necessary evil; anti-war proponents question the "necessary" part. Garlemald hiring Roegadyn battlemages to defend themselves against Hyuran raiders is probably necessary; Garlemald using magitek to conquer two and a half continents is probably not.
There's also another incident that may or may not rise to the level of "atrocity", but is generally seen as pretty terrible. Before Ul'dah and Sil'dih were formally founded, the eventual prince of Sil'dih used the aetheryte network to ambush his enemy. The eventual prince of Ul'dah then destroyed an aetheryte while it was in use, causing eight hundred enemy soldiers to vanish without a trace.
This was seen as unconscionable enough that the Sharlayans, who set up the aetheryte network in the first place, shut down the whole thing until the civil war ended. I would not be surprised if this incident contributed greatly to Sharlayan's current isolationism, and its belief that Eorzeans are all warlike barbarians. After all, we clearly haven't shown any marked improvement in the six hundred years since.