Yep, you are correct. There is no other way to explain everything about Kreia in the game. I needed to check the definition of a darksider to make sure, and it does fit with what you say. However, now I can't see how most of the dialog choices in the game that give you alignment points are able to alter alignment at all. Since in most of them, you are expressing your own opinion, not acting through the force while drawing power from either "good" or "bad" emotions. Following this trend Kreia would indeed be gray, since she orchestrated the elimination of both the Jedi and the Sith.
As for what Vash says... if the bond between the Exile and Kreia is considered to be of the same nature as the one between Kaah and Vash, then the only explanation can be that a bond fades when a certain harmony between both people (their alignment being equal) is broken, which never happens with Kreia and the Exile. However, it is way easier to assume either that Vash was simply wrong (but then why did her bond with Kaah break?), or that the bond between the Exile and Kreia is something special.
EDIT: Oh, and... if with "through Visas on Dantooine (and there are her darkened features as well)" you meant the scene in TSLRCM during the council confrontation, you should know that that aspect of the scene is not a restoration.