Was the N-word an offensive word in Mark Twain's day?

The Daily Show recently did a bit on this issue, and the interchange between John Stewart and Larry Wilmore explains the tension around the "N word" and the US tendency to indulge in revisionist history.

Here is a partial transcript:

...

JON STEWART: Well, the editors of this new version are trying to make the book more accessible, they say, so that it can be taught without making students in the classroom, who may be uncomfortable, repeat the word nrnrnnrnrnrnr….

WILMORE: I’m sorry?

STEWART: Just so that the children don’t have to say, in the class, say nnrnrnrnernnnrr….

WILMORE: I’m sorry, what word were you…

STEWART: Nnnnnuuuuuuu….

WILMORE: Say it, Jon!

STEWART: Nnnnniiiuuuuuuu…. It’s uncomfortable!

WILMORE: And it should be! Look, Mark Twain put that word in for a reason. The n-word speaks to a society that casually dehumanized black people; “slave” is just a job description. And, it’s not even accurate! In the book, Jim is no longer a slave. He ran away! Twain’s point is he can’t run away from being a nigger.

...

Many people in the US feel extremely uncomfortable with the "N word" because of its checkered history and negative connotations, though the word was much more commonplace at the time that the story was written. The common term for African American ethnicity was derogatory and dehumanizing, so Twain went with the common term as a sign of the times.

Another item of note is that the term "Injun Joe" was changed to "Indian Joe", and that appears to have garnered considerably less attention, despite being a similar switch.

Etymology Online has this quote:

From the earliest usage it was "the term that carries with it all the obloquy and contempt and rejection which whites have inflicted on blacks" [cited in Gowers, 1965]

and then goes on to state that

But as black inferiority was at one time a near universal assumption in English-speaking lands, the word in some cases could be used without deliberate insult

I will refrain from speculating what Mark Twain was indending when he used the word, as I'm no expert on things Twain. ;-)

Based on several articles I read in the aftermath of the "n-word translating to slave" issue, it seems that it was indeed a derogatory epithet chosen deliberately by Twain for the way it reveals southern prejudice, but it was apparently a common, uncontroversial word in everyday speech. See Prof. Thomas Glave's reaction

While Twain would undoubtedly reject efforts to whitewash his works of controversial words, he would undoubtedly be proud of a society that has progressed enough in racial tolerance to have become uncomfortable with a word with such negative history.