1. Parent comment's dismissal is based upon details revealed in the article, or rather details that weren't revealed. He suspects that, since the victim escalated immediately, the victim may not have wanted a peaceful resolution. We don't have the full picture, but what we have suggests that there were other ways to handle it.
2. Yes, I expect you to say that you're upset by the situation. I cannot read your mind; most people can't read your mind either, and many of them don't know the line between a 'joke' and harassment. Telling someone you don't like what they're doing is a crucial step, because otherwise they may assume nothing is wrong. We want the boss to learn that his joke is not funny, and to do that sometimes you have to say it to his face.
3. Neither side is communicating well, which is indeed why HR exists. It's also possible that the boss would've continued after being told explicitly to stop. This does not mean you reach for HR's hotline the moment something goes wrong. You don't respond to a slap by pulling a knife, and you don't respond to a knife with a nuke--at least, not without examining other options.