It is cannon that the Exile is female, which means that the Handmaiden didn't join the party. So that makes her being the 3rd Darth Traya unlikely.
I support Revan as a betrayer. It is easy to understand that he could have faked being a LS Jedi again to destroy Malak, and use the Republic as the means to destroy the only threat to his reign as the Dark Lord of the Sith: the True Sith. So after this becomes apparent, and he uses the PC to eliminate the True Sith's leader so that he can take the throne, the PC must stop his attack on the Republic.
Just my idea.