That's because Kreia used her "forget me mindtrick" on Atris and the other Jedi Council masters... she confesses that if you ask when having enough Awareness...
Also, she was exiled because the council blamed her for the fall of Revan and during the Jedi Council Exile of the Exile they also spoke about how "her" students all fell to the Darkside and were all failures, hmmmm...
And if Handmaiden enters the ship you can ask Kreia "You seem to hate the Handmaiden, why is that?" and then she plans to use her as a pawn to lure out and expose Atris. Not exactly what one would do to their daughter, no?
And about why she does not wish Handmaiden and Exile to interact... well, she also doens't wan't Exile to get intimate with Visas, does she?