iPlissken

Realizing that this is years later, but I had two ideas about Kreia being at the council that make her dialogue with Atris make logical sense. The first is hinted at when you arrive at the Polar Academy on Telos. Atris is unaware that Kreia is with you. Likewise when you confront the Jedi Masters on their respective planets they are unaware that she is with you until she reveals herself to them on Dantooine. So it is certainly plausible that she manipulated Atris and the Council after the war and they don't remember. The second is simple: Kreia is a Liar and Manipulator. She's lying or manipulating Atris in order to push her to the Dark Side, because as we saw earlier, she could easily hide her presence or her true self from Atris. The fact is, it's very difficult to piece together Kreia's motivations or her plan because she does conceal so much from you. We don't know the facts of anything that happened between the war and immediately before the story begins, but we do know that the logs on the Harbinger suggest a different reality than what HK-50 and Kreia told you on Peragus. That could be chalked up to bad writing, but we do know that both of them lie. For all we know, Kreia's plan to destroy the force dates back many years before the war and that she has been manipulating events since then. We do know that she was exiled before the war, because she was thought lost during it.