Did seeing Lorelai and Rachel becoming friends bother him? It was just that Rachel was someone from his past who he wasn't even sure was going to stay. And Lorelai was someone who would always be there for him. They were such different people, and both amazing women. He tried to explain this to Lorelai, but it ended up coming out wrong as it usually did.
Then he realized that they had been talking about him. He didn't want Lorelai involved with his relationship. And he didn't like the fact that she was so eager for them to become serious.