I think that the most probable explanation is simply that Revan left for the Unknown Regions and did not know.
I can't remember exactly where, but I feel I remember a discussion on the Bioware forums (will look for a link!) where a dev said it didn't go any farther than kissing on the Ebon Hawk black screen moment. Yeah, the "we shouldn't have done that" line is a little out there from our perspective, but Bastila is:
a. loyal to the Jedi Order, aka probs hasn't been snogging very much.
b. kind of frigid in general.
You also have to remember that KotOR was made by BioWare, TSL was made by Obsidian, and TOR is being made by BioWare. Therefore, it's possible that BioWare had the intention of a Rev/Bas child, but never got to expand on it because they didn't make a direct sequel. Obsidian basically ignored the Rev/Bas relationship, aside from small little hints ("oh master, I love you but I hate all that you stand for, but I think we should go press our slimy, mucus covered lips together in the cargo hold!") It's not shocking that three games made by two different companies have some discrepancies. It's also quite possible that Bastila hid the child, I mean she
didn't even come out to meet the Exile (if I remember correctly), the child would clearly be very powerful; since the Exile's intentions may have not been known, showing two of the last Jedi (well, one Jedi, one future), for that matter very strong Jedi, might not be a wise move.
Revan's loyalties have always been with the Republic first. Even if he did know about Bastila being pregnant, I could see him leaving for the good of the Republic.
Of course, I've always found the "baby is conceived through the Force" thing a bit ridiculous, so I might be more inclined to think Bastila and Revan got down & dirty.
Edit: Found the thread:
"but the Bastila romance does let the PC sleep with her. That got added much later, believe it or not, when it was felt that the Bastila romance really felt like it vanished considering what happens to her...
"...And you actually sleep with Bastila?!! I thought you just kissed. I would think she would have reacted more drastically about actually sleeping with you, rather than just saying we shouldn't have done that and then run off...
Personally I would have prefered it just being a kiss. I don't remember something like that happening in a Star wars story for one thing.
First of all it doesn't even seem reasonable to sleep with her because basically just right then you actually fully know she has feelings for you."
"Hmmm... come to think of it, it might just be a kiss. It *is* all implied, after all, so you can suppose whatever you want...
So not really confirmed or denied.