DOUGLAS: You can’t just apply to one place.
NATALIE: Chilton wouldn’t allow that.
LORELAI: Is that true?
RORY: Pretty much.
Chilton would certainly not permit Rory to only apply to Harvard. It is staggering that Lorelai wouldn’t already know this – she did attend a private school, even if she never ended up applying to university. And even if she somehow didn’t know this from her school or her parents (surely Richard and Emily would have talked to her about college?), it’s something which she should have educated herself about if she wanted to help Rory get into Harvard.
It also seems very telling that Rory has never talked this over with Lorelai, but kept her college applications a secret from her mother. It seems that she was so nervous about how Lorelai would react that she never discussed it with her. Lorelai’s overreaction at dinner shows that she was right to be wary about it, but then again, Lorelai probably wouldn’t have overreacted so badly in public if Rory had talked about it with her first.
The Annotated Gilmore Girls 