I have been thinking about this article since I first read it and commented on it three months ago. I think you're right that we shouldn't assume that the canon of studied books is sacred and unchangeable. We need to have our children study the works of great black writers, not just great white ones. Unfortunately, those are precisely the sorts of books that are more likely to include the N-word. So it looks like a dilemma caused by a forced choice between hurting the feelings of young black students and cutting them off from the literary acheivements that would instill pride in those students.
I think the way out of this is to attack the inference that if someone said something in a book, it must be OK to say it in conversations. This is obviously false if you think about it. It's OK to write a book that contains the sentence "Put all your money in this paper bag, or I will shoot you between the eyes." It's not OK to say that sentence to someone in conversation. There are also words that certain people are allowed to say, and other people are not allowed to say. Ta Nehisi Coates points out that I am allowed to call my father "father" and you are not, among many other examples. There needs to be at least a day in which students are taught these distinctions, and told in no uncertain terms that they will be punished if they don't observe them.
That being said, I think there are problems with creating social norms around forbidding certain words. That doesn't invalidate the problems you are discussing here, but it does create a dilemma we need to think about. I discuss this dilemma here.
https://teedrockwell.medium.com/the-fall-and-rise-of-forbidden-language-bb0a27152b09
Steve QJ also has a take on the N-word which I think is worth considering.
https://level.medium.com/this-is-the-way-the-n-word-dies-ab51167bf9d0