LORELAI: Whoa, whoa, whoa! There is a baby here desperately in need of some bath water.
A play on the common idiom, “To throw the baby out with the bathwater”, meaning that in the rush to rid oneself of unwanted things, valuable things are being lost as well. It was originally a German proverb, dating to at least the 16th century.
Lorelai means that just because Margie can’t be Richard’s secretary any more, it doesn’t mean he needs to give up on the idea of having his own business as well.