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.