The last time I remember it got this heated on the story was when chandra and nissa performed the equivalent of a channel fireball on ulamog and kozilek. Which was also framed as a war between the inhabitants and an alien, off-world, threat.
The victory, while grandiose in presentation, it doesn't sit sell with the audience and that the audience might feel the experience was cheapened. Its understandable. The eldrazi and nicol bolas share in common they are meant to be so powerful and beyond mortal comprehension, that winning against such threats should feel nearly impossible. But when not handled with careful writing, such characters act as a trap for writers, which they sprung with nicol bolas.
With nicol bolas, the expectation is that he has his initial plan with an untold amount of backup plans meant to secure his victory at any cost. When that illusion becomes broken, that is when the audience feels wronged. That the expectation is when you have exhausted all of his backup plans, he is truly vulnerable. If he didn't plan for Liliana to turn on him even though contract bound to him, that is a crack in his illusion.
It is not about the audience simply wanting one side to win, its the journey to that victory.