Actually the more I think about it, Kreia/Traya hated how everything was manipulated by the Force. What she possibly saw in the Emperor was someone who's actually risen above and could manipulate the force freely. Considering that she willingly sacrificied so much of herself for the Exile oh so long ago just to prove points and have incredible powers of foretelling, I wouldn't be surprised that she allowed herself to be captured/manipulated by other Sith like the Emperor and Darth Baras. She clearly knows how to play the long game in view and would undergo all kinds of torment to finally get to her goal. Even so, I still have doubts that the Entity is Traya and would hope it could be cleared up eventually