I always assumed that the black screen at the end of the Bastila romance implied a little more than kissing went on. That at least would justify her whole "we shouldn't have done that". I guess Jedi don't know how to use protection (No, "trusting in the force" won't work).
I love the last part with trusting in the Force
To help clear things up....
Revan did not leave till about a year after the events of kotor1. During this time he was getting deams and visions of what believed to be his past,..most likely about the Sith Empire and how he was turned to the Dark Side which Bioware is now hinting the turn of Revan was not a natural one which is why the Jedi Council did such a drastic way of entering the former Jedi's mind to repair it.
Also during this time I can assume that Bastila and Revan were continuing their relationship...openly or not openly is not clear. During this time Bastila got pregnant. Not on the Ebon hawk (They still might have had some alone time) only because that means Revan would know that Bastila was caring his child which might have affected his choice to leave Bastila and the Republic for this threat.
This is why kotor2 takes place 5 years after kotor1 and Revan left one year after kotor1 which means 4 years before kotor2.
I hope this helped