Well considering I have seen many conflicting reports about watcher 2 romance in the prologue, I made a playtrought just to check how to do that in the so called prologue.My first agent was a chiss, and she denied my at the end of the Dromun Kass mission. However, when I played a human, she seemed much more open to me, and so I picked every flirt option incluing the one that you have in samara's mission.If you ask her about how you can go,you will have a "secret" flitrt option,where you will then be able to tell watcher that you might need to get close to samara, to wich she will respond that it's part of the job, and that she won't mind.Samara is also romancable if you pick the two first flirt option, but not for alien apparently, since my chiss was denied too when he tried that. Lastly, you can sleep with her at the end of the Dromun Kass missions,if you have taken all of thoses flirt options,and if you have spoke to her and flirter with her as part of the optional mission "understanding intelligence". It should be said that I removed Kaliyo(yet I flirted with her on every ocasion) from my party every time I had to speak to anyone for the story classes,especially in the briefing room (with Keeper and all of the others).Also, light side has nothing to do with it, as I was neutral. This leave two things,either the game does'nt allow you to romance her if you are not human,either it is the prescence of kaliyo that cause her to reject you.If anyone managed to sleep with her in the prologue while being an alien,feel free to correct me.