My thought is: It's just a word. It's not a polite word, and I don't use it in either public or private speech... and that's true with a number of words. However, it doesn't have special powers. It shouldn't be treated like "Voldemort" in the world of Harry Potter in that it must not be even uttered. Hearing or seeing the word doesn't cause irreparable harm to anyone. It won't curve your spine, cause fits of the vapors, or anything else.
As for the novel in question, I understand the historical context of the usage. I don't think that it's hard to teach children that context. I also wonder if one of the pivotal mini-series of my youth, Alex Haley's Roots, were to be remade today, what treatment "the N-word" would received in the updated version?
So, if they want to "white-wash" Tom Sawyer, then I guess so be it. I guess it doesn't change the story line, but it certainly limits a bit a middle-schooler's understanding of the culture of post-Civil War Missouri.
So the "N-word" is out, but the "I-word" still OK in that Twain work?