Harbinger Captain: "We have taken on passengers to Telos..." The Exile was not the only passenger that the Harbinger picked up. It is possible, though I find it unlikely, that Kreia was one of these passengers.
This is what I've always assumed, that there was another ship (a small one like Bastila's G-wing in K1 or something). Simply because of this line: "When we intercepted the Harbinger, it was crippled, drifting in space. It was a simple matter to board the vessel and rescue you. Unknown to me, however, the Sith were already on board." If they (who is this "they", btw? Kreia wa