While personally, I think this is a entirely legitimate direction to take with the story, I'll point out that on some level those 90 chapters of relevance can exist for the purpose of heightening the impact of the character's removal.

It's entirely possible to deliberately write a female character who exists purely for her death to motivate a male character (or vice versa, but it's likely that fewer people would complain,) who's well developed and active in the story for a long time, if the author is doing so simply to set up the extent of the motivation. And I think some people are concerned that, given that Eliezer planned Hermione's death from the very beginning, this is just what he did.

I would be shocked if someone were criticizing comic books for too much planning and coherence, if the Fridge critique referred to the character as a whole rather than her death. So in part this seems like a non-sequitur.

Back to MoR, the "major story arc" could indeed lead to Hermione doing something awesome, and her apparent death might not destroy that possibility for the sake of Harry's character development. But right now, you're dismissing the criticism out of hand because of an arc that led some readers to call Hermione silly. You're talking about a story that led people to question her characterization before now.

As far as malign coherence goes, Eliezer chose to throw in a dig at some strain of feminism during "Self Actualization," which ends with Harry and some men saving Hermione and friends. Now, Eliezer has said that he made SA longer than it strictly needed to be because he didn't realize he could take a different road to setting up (an arc where Harry saves her again, and she suffers and feels incompetent and stupid before her apparent death). But in a finished work, it would look like he put all this in for a reason. And looking back from chapter 92, a lot of it does in fact look like deliberate trolling of feminists.

Were this a finished work, certain feminists reaching chapter 89-92 could reasonably delete the file. And if I told them that later chapters improve the issues in question, I would not expect to be believed without major spoilers. Because I'm more like (a dumber version of) Eliezer than they are, and I still don't know what the Hell he's doing.

That's not what fridging is- it refers to a specific type of death, where a female character is killed by a villain and left for the hero to find, specifically for the purpose of affecting the hero mentally. We don't know yet who killed Hermione and why, but it's possible that it was meant as a fridging.

TvTropes:

A character is killed off in a particularly gruesome manner and left to be found just to offend or insult someone, or to cause someone serious anguish. The usual victims are those who matter to the hero, specifically best buddies, love interests, and sidekicks.

I think it's a bit absurd to call something a "fridging" when the character in question has been around for 90 chapters and had their own major story arc, etc. That's really getting away from the spirit of what the "women in fridges" idea is complaining about (ie women who only serve to die in order to motivate the male characters).

That might have some validity, but the validity is detracted by the difference in scale in what Hermione and Harry have dealt with. Harry has been discovering new magic (some small amount with Hermione but only because he helped), destroying avatars of death, rescuing people from prison, putting the son of the most evil person around on the past to redemption. Hermione's arcs consist mainly of fighting school bullies, and even doing that to a large extent with Harry handling a large fraction of the problem, and occasionally beating Harry in a mock combat situation where he was clearly holding back. It is also noteworthy that Hermione's death occurred after there were already largescale complaints about the role of women (and Hermione) in the story. And Hermione's death didn't even accomplish much: she wasn't saving the life of another student for example (a student getting in the way of the troll would have been an obvious thing to matter), and despite all her intelligence, she never in the course of her arc developed new magic or the like.