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 wasn't alone?) intercepted the Harbinger and the Sith were already on board that means the Ebon Hawk was already on board the Harbinger. So she couldn't have been on the Ebon Hawk. It also implies that Kreia was not on the Harbinger, either. That leaves only one other option, the aforementioned ship.
The prologue is actually incorrect about the use of a hyperdrive. As I understand it, hyperdrive is only used to jump from system to system (ex: Taris to Dantooine in K1) Sub-light engines are what get you around insystem (say like when you come out of hyperspace at Telos and fly toward Citadel Station those are the sub-light engines at work) and these would be what T3 would use to get to the Peragus mining facility. Anyway the hyperdrive may have worked long enough to get from where the Harbinger was to Peragus then conked out.
Edit: I doubt the Exile was naked on the Harbinger. The medical officer on Peragus was most likely the one to undress the Exile when she put him/her in the kolto tank. What she did with the Exile's clothes is a mystery though.