I don't like to think that a word can have inherent offensiveness. Offense should be taken on a case where words are used offensively, not because of some kind of taboo vocabulary. It's all about context.
If I were to say "i don't like that weeaboo stuff" or "you're a weeaboo" I wouldn't expect people to get offended by the word "weeaboo" because I see no inherent offense to it. If I were to say "shut up weeaboo" in a completely serious manner, it would be offensive because a) I imply negativity toward being a weeaboo, b) I dismiss what the person is saying, supposedly because they're a weeaboo and weeaboos are bad, and c) I'm just being a butt and people don't like buttmen.
I don't quite believe in the concept of a "slur" because the entire point is that it is inherently offensive to a group of people. I can respect if people take offense to something, but it's absolutely asinine to cater to this on a scale where you're making general statement with millions of possible recipients. If you're being blatantly offensive, that's one thing; if you're just using a word some people might not like, that's another.
I certainly wouldn't say Jon has handled the situation correctly, but the entire thing was conceived from hypersensitivity and aggressiveness, and that is not okay in any context I could imagine. Especially if the people are making an active decision to involve themselves so they can kick and scream and try to get the world to comply with their problems. If I were in his place, I would've just left it alone and never replied to the guy in the first place. If it blew up anyway, the best way to handle it would be to say that no offense was intended. Any continuing controversy would be out of my control; there's nothing more for me to do.
blah blah blah yelling at the television the internet cares about me and my thoughts