I don't know that the people who leveled accusations against this guy are completely equating "usage" and "meta-usage".
I do know that there are people who view "meta-usage", particularly in casual conversation, as problematic. The n-word is viewed by them to have connotations of severe power imbalance and violence, particularly in the mouth of a white person. The idea that they should have to hear the word in casual conversation, without warning, whether it's intended to wound or not, is contentious. Intent matters, but so do the words themselves. To put it in your terms, some words cannot just be "stripped of meaning" to some people.
I personally empathize with people who feel this way, despite being a white guy for whom no such word with such visceral effect seems to exist. Even if discussing racism in a conversation, I probably just wouldn't whip out a historical quote from someone that happened to have the n-word in it. And I don't think that's as ridiculous as you're making it out to be.
Nobody is suggesting that contextualized, or (ideally, to some) forewarned, meta-usage will never have its place. But that's not really what happened in this story, is it?