Rory was so upset over her fight with Jess that she stayed with Emily overnight. When Lorelai asks to speak to Emily, Emily tells her what she really thought of Jess – she was horrified and disgusted by his behaviour, and thought he was abominably rude. She is also still angry about the car accident, which she completely blames Jess for.
Just as Richard saw Dean as not good enough for his precious granddaughter, Emily sees Jess as not good enough for Rory. But she is taking her own advice to be polite and welcoming to Jess, because she doesn’t want to alienate her granddaughter. And of course, it is all Lorelai’s fault for allowing Rory to date Jess!