Endwalker is the most controversial expansion

[Dikatis]

You seem to be conflating the Garlean people with the Garlean military/government. You're also rather handily forgetting that the vast majority of Garlean military personnel were in fact conscripts, and that a lot of the ones stoning people and laughing were those selfsame conscripts.

...I don't think a conscript would have a Garlean helmet with a third-eye slot and wield a gunblade. "Just following orders" and "indoctrination" stops being a excuse when you willfully disregard acts of violence on the citizens you're supposed to protect, especially under the egalitarian Gaius van Baelsar.

To the subject of the EE: A few key details:
1.) Nael, who had as mentioned before been directly responsible for keeping the project alive in secret, in fact lied to the Emperor by claiming the weapon could now be controlled.

And yet no Garlean but Gaius and Varis have ever expressed any misgivings about it?

2.) Note the aforementioned cleansing mentions only beast tribes and eikons. The beast tribes, barring a select few (who the Garleans had no knowledge of anyway), were believed to be tempered to the last. This particular point comes up in-game on a multitude of occasions. Solus and Nael aside, all participants at this time believed it could indeed be controlled.

This is objectively untrue as Garlean forces employ the Kojin of the Red as mercenaries to hold control Yanxia and the Ruby Sea. Dalamud is, by all counts, deployed as a weapon of genocide against all the peoples of Eorzea.

3.) Only Emet-Selch, who we now know was Emperor Solus, and Nael knew what was really inside Dalamud. Everyone else was completely in the dark.
4.) Obviously, Emet-Selch planned all along for Bahamut to be unleashed at the appropriate time. It was always going to happen, and not for the betterment of Garlemald. It was all for the Rejoining. They lost a lot of troops that day.

But it was still employed as a weapon of genocide. That's objectively true.

The Twelve were regarded as nothing more than eikons by the Garlean Empire. Much of the Ala Mhigan's culture revolved around their worship of Rhalgr, including their rather violent past. Despite that violent history and nearly their entire culture revolving around one of the Twelve, they were allowed to keep a good of their identity intact.

And yet again, Gaius van Baelsar stomps out religion, only to deal with an ashkin uprising due to his campaign to wipe out even the most innocuous forms of religious expression. Which is even more hypocritical when you see that Solus is laid to rest at a wake, showing that Garleans have their own burial rites.