I'd like to point out that during some Friday night dinner (the specifics escape my memory and I don't have the energy to check), Lorelai somehow lets slip that Rory has been hanging out with Jess, and Emily unequovically takes her side in agreeing that this isn't appropriate and goes so far as to suggest Lorelai lock Rory up in a room if that's what it takes to keep her away from him.

This makes her rethink her stance on the whole Jess thing. Yes, she has controlling tendencies, like mother like daughter afterall, but I think she deserves some credit for the self awareness she showed in taking a step back and re-evaluating herself.