My guess, is that like numerous other things in TSL, discovering that Kreia is Kae was cut content, or possbly not even finished by the time of TSLs release. It is true that the Handmaiden's role is limited, though I don't see what that has to do with it. Can you please explain, Shem?
Well, yes, Kreia claims she was thrown out because of her beliefs, but it would not be the first time Kreia lied, would it? What is important to remember is that people change. Shem is absolutly right in thinking that Kreia certainly would not be following Revan to war. Possibly the war changed her, but that is just speculation.
Did Handmaidens mother give her to Atris, or did she just end up there because she was a half sister? I honestly don't remember the answer to that. If HM says her mother left her there, then Shem has made a good point.
I choose to believe that Kreia is Kae because of the evidence presented in Ravnas' link. Each one of those scraps alone can be easily debunked, but all together...hmm, thats a lot of coincidences, too many to just brush off as circumstantial IMHO.
Viva La Resistance!