Actually, Jon is insulting you because you murdered his brother.

I could never kill Belethor. His voice actor is too awesome. And of course, when I see Belethor I see a proud Enclave soldier fighting for America.

How does he know that I killed him when I turned into a werewolf for the first time, and I received no bounties over my head? How could he possibly know that I killed him and not someone else? Wouldn't word get around that I'm a werewolf, and that the entire city of whiterun would want to kill me as a result?

It's probably something in the AI like when you're sneaking and/or invisible during which you're not detected, but the NPCs keep looking right at you.