I actually always questioned why k*ke was used, but he used the word brother instead of n*gger. I dont think the controversy would have been anywhere near as bad, but using just one very no no slur against a different race or religion.
I think if MJ had used the N word, it would have been so powerful coming from Michael Jackson, in a song highlighting the injustices minorities face. It's powerful already, I just thought it was an odd choice to hold back when referring to his own race when it would be a lot more closer to home for him.