1. Kurt wasn't going to tell anyone even before the death threat. Also he had a chance to tell people why after the threat in Furt but he still didn't tell them. Why? He was around lots of people to protect him. Maybe because he doesn't like outting people. Yes it's stupid and if I was in his position I would of told but Kurt didn't.

2. It was implied that this apology wasn't going to happen in that scene. It was Kurt talking to him that made Karofsky cry. Kurt telling him that he see his pain caused it. I'm pretty sure that Karofsky didn't plan that apology at all.