No one is saying that. What we are saying is that some of the methods employed by Eorzea are pretty horrible. Continually lambasting the Empire for doing awful things while at the same time ignoring the fact that Eorzea has committed more than a few atrocities of their own is not a type of writing everyone is going to enjoy.
Try to look at this through the lenses of politics and cold logic without any emotion thrown into the mix. Legally speaking, a country that is conquered by another country is in fact recognized as part of that country. Even Great Britain acquired the vast majority of its lands through conquest. To invade any of those lands is to invade Great Britain, and they will retaliate as they deem appropriate. Garlemald is no different in this regard. Those lands were won by shedding of Garlean blood, sweat, and tears. They've got every right - nay, an obligation - to protect what is theirs. I don't believe I've seen anyone deny that the Empire has done some fairly terrible things. The fact that the people in the conquered territories got assistance in taking their land back is also fine. What isn't fine is the assumption that Garlemald shouldn't retaliate when it is being attacked. The Empire, as a nation, should by all rights do anything within its power to protect itself. If manpower and technology are no longer enough, then yes, it is perfectly reasonable for them to resort to using something as terrible as Black Rose. It isn't as if the Eorzeans haven't been burning, freezing, electrocuting, poisoning, rotting, and exploding Garlean troops all along.
The Garleans - including Varis - did not possess this information. They saw it only as a weapon they could employ, and they only decided to employ it when backed into a corner with no way out. The issue is who they used it on. Killing the non-combatants was a bit much, though such a thing is inevitable in war. One cannnot hold the Garleans responsible for something that hasn't even happened yet. As for a meteor cast by a mage? I encourage you to look at the sheer size of some of the meteors that have been dropped over the course of FFXIV. A space rock of that size would in fact be quite the catastrophe. Then there was the War of Magi. There are areas of the Source that cannot support life to this day because of that event - not only because of the catastrophic damage done by magic itself, but also due to the sheer amount of aether consumed by all that spellwork.