Wookiepedia states that she did in fact have a larger place in the game:
- The name of her appearance set is Party_NPC_Atris.
- She has an unused party member portrait in the game files.
- As said before, she is the face of TSL in the marketing department.
- Atris as Darth Traya is still viewable by editing the CurSithLord=1 option in the swkotor2.ini file.
- There were a couple of other endings where Kreia would be redeemed and Atris would assume the Darth Traya getup.
I understand this would be a major undertaking with lots of added content and completely retooling the end game sequences, but would it be possible to restore Atris to her original place as a party member?