Rolling into the party mega late here but... when does the story ever paint him as a hero? I didn't get that impression at all. There's absolutely nothing heroic about anything he does, and I don't recall him ever even claiming to be heroic at any point. His (almost) final words to us were something along the lines of making a world where heroes aren't needed - he seems to have come to detest the very concept of the hero.
I didn't feel like they ignored the implications of what Emet did to Vauthry and his mother. That whole segment was horrifying. What he did to them was horrifying, there's no denying that, and I didn't get the impression that the story was trying to.
What the writers did was give Emet motives and drive, reasons for his choices and actions - ends that he felt justified his means. He's committed countless atrocities, for a cause he felt justified that cost. I've said it before somewhere on here, but I genuinely didn't get the impression that he honestly believed all those lives were worthless. Maybe I was reading into it, but I think a far more interesting interpretation is that Emet had to convince himself that they were worthless. Because if they were worthless, then the wholesale slaughter of millions doesn't mean much - they were just ants, after all, so he doesn't have to face what he's done or what he's become. From our (character's) view, that's probably full on delusional and arguably evil, but that reasoning is what makes him an interesting character imo. He's a villain, and a monster, but he's a monster who thinks he's right.
At the end of the day Emet's death was necessary, but imo his story - his people's story - absolutely is tragic.
Edit to add a bit: What got from the story was that Emet was an ancient, bitter, angry old man who'd convinced himself he had no choice but to carry the weight of his peoples lives and memories on his shoulders, and that the only way to honor that memory and to restore the world he'd lost was to utterly destroy the new one that had been created. What happened to his people was horrific, and he's suffered horrible loss, and if taken entirely by itself his goal could even be called noble - to bring his people back to life. His logic is twisted, warped by the belief that his people are better, more valuable, more perfect, and that the new life of the new world is unworthy to take up their mantle. And the impression I got was that the writers were saying yes - this is horrible, and tragic, but this does not justify his actions. His people are not better or more valuable - they are just as flawed and imperfect, just as capable of mistakes and bad choices and hubris and arrogance, as we are. Emet-Selch is wrong. That's the message I got from his story. Not that he should be hailed as a hero.