She had a 3 second cameo, and it would have made no sense at all if she didn't show up.
Yes, I suppose you could probably kill her even as a Light Side jedi. However, since the developers aren't going off of a save game file, they have to make certain assumptions, and the assumptions that they've made have generally been positive ones (as evidenced by the developer quote that if you skip the relevant questions early on in the game, then Revan is automatically male and LS). So the developers are going to operate under the assumption that you didn't kill her, which particularly makes sense given the link between the two. Mental links probably do funny things to your way of thinking that can't be duplicated in video games.
imo, given who she is, and her link with Revan (emotional for a male Revan, and mental regardless of gender), she would probably be even more concerned about his location and well-being than anyone else in the first game (and still fairly concerned about the location and well-being of a "her", albeit not quite so much), and it would be rather silly to have Carth make his cameo appearence, and not slip in Bastila at some point.
There's also the fact that if they don't put Bastila in somewhere, then people will speculate that she went with him.