I do think she was planning on being a force ghost even before the final fight in K2, but truthfully, I don't think she was referring to herself in saying that there would always be someone who knows of betrayal as a Darth Traya. There are too many parallels and wierd inversions between her and Ben Kenobi for her not to become a Sith ghost.
But no. I do think her reference to there always being a Darth Traya was an oblique reference to something she wasn't a part of that Obsidian already had plans for. I don't think it makes sense for it t be Bao - Dur or Atton, because Kreia also said that their futures are shrouded in mystery to her. She spoke of the new Darth Traya with something approaching certainty.
"If force is the game, the murderer wins over the pickpocket." Ayn Rand
"Justice is the midpoint between being treated unjustly, and treating others unjustly." Aristotle