It could be they meant "hero" in a sort of squint sideways and think symbolically way, but apparently enough people took the wording at face value that Yoshi-P had to remind us the Ascians killed billions, and calling Hydaelyn the evil one was shortsighted--so I would count that as a failure of the writers in conveying their intent. There were better ways of expressing how tragic the Amaurotines' fate was.
The "moral relativism" line definitely conveyed how little Emet-Selch thought of the lives he was seeking to destroy, but since the writers were pushing for sympathy for him, it also sounded a bit like excusing him. It certainly was taken that way by some players.
And the writers are very selective who gets that sympathy, even if they do equally horrible things. I wouldn't say Zephirin was a nameless mook, but Zenos has no higher motivation than relieving his "boredom". Thordan, then? He was the driving force behind much of Heavensward, he thought his actions were just for the preservation of Ishgard, but there was never any doubt in the narrative that he was wrong. After he and the mooks were dealt with, there was no mention of any of them being heroic in their efforts, no requiems to commend them for it. All that, and their atrocities don't even put a dent in the scope of what the Ascians committed.
The writers also seemed to try a similar sympathy thing with Fordola in Stormblood, but that went over like a lead balloon, thankfully.
TL;DR: The charisma of an antagonist is all well and good, but the writers shouldn't really lessen the impact of the evils they do for the sake of it.
As for Vauthry, quoting the Innocence Triple Triad card, he was "corrupted by the power of a Lightwarden whilst he was yet a babe in the womb". Considering how a Lightwarden twisted Titania from a benevolent ruler to everyone's favorite trial, it seems a very safe bet that Vauthry's actions were entirely of Emet-Selch's making. It was established that no one short of the WoL could resist the corruption of a Lightwarden, and it was only by Hydaelyn's blessing that we resisted it for as long as we did. Trying to hold Vauthry responsible is like blaming Thancred for the massacre at the Waking Sands.
But the writers, although they showed the player the truth of the situation by the Echo, never allow us to reveal it to anyone. Instead, we are simply made to smile and nod as usual when the driving narrative of Eulmore even in patch was "man, Vauthry sure was evil". The writers hold one of Emet-Selch's victims to a higher standard of conduct than Emet-Selch himself, and there seems to be no actual reasoning for it except they favored him. So for me, at least, it felt very not heroic to remain silent on that situation alone, yet be nudged by the narrative to convey sympathy towards the actual cause of the evil. Not just sympathy, either, but to accept the narrative that he was heroic.