The Doman and Ala Mhigan territories were liberated; ergo, the Eorzeans were well within their rights to defend them from Imperial aggression started under false pretenses. The conflicts that led to their liberation were over for some time before the next battle, during which Ala Mhigo hammered out a new system of government and Doma received an Imperial ambassador. The Alliance pushing into Imperial territory after the Ghimlyt Dark in the original timeline is not an effort at conquest, but an effort to stop Varis from causing rejoinings on purpose (this would cause the complete annihilation of multiple other realities with the deaths of countless people on the Source besides). The Empire is fully within rights to defend its territories, but it's not as if the Alliance can just sit around twiddling their thumbs knowing the ruler of the Empire is deliberately planning to commit genocide multiple times over (and they learned this in a parley with him, so it's doubtful further discussion would do any good). Knowing this, what would be the correct course of action?
The GNB NPC is another example of the reviled "apologist defector," though. Supporters of the Empire don't like such characters. (The GNB quest also reveals that some Imperials use shock collars to enforce obedience from prisoners. Or just for funsies.)
Weapons like Black Rose are not weapons of war. They are weapons of terror, intended to intimidate others into submission instead of actually being used to prove military superiority or, failing that, just kill the opposition without giving them a chance to fight back. That doesn't prove anything but that you're capable of killing lots of people with chemical weapons, and dumping it on Eorzea (or any other region for that matter) is literally genocide. That is not warfare or securing borders, it is straight-up genocide.
We do not know how far the Alliance made it into Ilsabard before the Empire used Black Rose in the original timeline. It was not stated they made it to the Garlean heartland or the capital. I would argue that it was used as soon as the Empire realized it was not going to win otherwise, but that is unknown.
I do not recall the game ever stating the Empire was getting desperate. They were still well secure within their borders and nobody from Doma or Ala Mhigo, or the rest of the Alliance, had any intention of continuing hostilities (again, see above). The war was started so that Varis' plans of causing all the rejoinings so he could make his perfect master race and overthrow the Ascians at the eleventh hour, not because they were "desperate." The first thing they did after the conflicts were over was to carpet bomb Dalmasca into oblivion for daring to rise up in the hopes they could follow Doma and Ala Mhigo's lead; this does not strike me as coming across as desperate or vulnerable. (Desperate for what? Vulnerable how?)
While war mages are part of Grand Companies, what we've seen of their capabilities are... rather unimpressive. It took all of the senior Thaumaturges of Arrzaneth Ossuary to create a stream of fireballs potent enough to crack open the gate to Ala Mhigo - this is all we've seen of such magic being used in a military capacity. The magic employed by the PC and the Mhachi Black Mages of eld is tightly regulated in contemporary times without pissing off the Elementals [i]as a consequence of the War of the Magi[i]; thus very few are able to employ such great power. Dropping meteors is not something every thaumaturge can do, and in fact some people can't even practice the arts at all.