Oddly enough, I'm not familiar with this game. But just from what very little you told me, it doesn't sound like a glitch.
There are numerous RPGs out there that have multiple endings. Star Ocean has around 80 of them, based on what you do during the quest. Even in some adventure games (such as Castlevania: Symphony of the Nights), based on how you defeat a boss and how much you complete a game gives you a different ending.
Granted, if I knew what KOTOR stood for, I could play through it and find out for real. If you know that killing Bastila would give you that ending, than don't kill him/her/it. If you still get the same ending, than there isn't much creativity there.
I'll try and see if I can find more info on it.
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You will walk in fire, earth, water, and air, through temptation, and at last into despair and desolation.
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