alright, just finished it (can't test it unfortunately though, as my computer won't play Kotor).
What it should do however is when you walk up to a sith trooper in the upper city, if Bastilla is in your party and you do not have the sith armor equipped, half of the sith in that module will attack you (I hope, if they don't something screwed up).
If anyone wants it so that all of the sith attack you as opposed to half, let me know and I'll make the change. (And if none of the sith attack at all, please let me know. As I said before I did not have a chance to test this do to my computer not being able to play either K1 or K2, therefore any playthroughs of the game I have to make must be done over at my grandparent's house)
you can get the mod here:
http://pcgamemods.com/mod/16419.html)