Sorry to be unbelievably sarcastic, but wouldn't it just be easier to ENJOY THE FRIGGIN GAME!
It's a game. It's Star Wars. Realism isn't a priority. Although you seem to think the actual films could have been done better as well, so really I'm not sure why you actually bother with Star Wars, but anyway.....
If you really want decent explanations of the KOTOR plot, go on wikipedia.
Regarding Kreia, I really think you've missed the point. The important thing to remember about her is that she loved Revan more than anyone. And if she thought Revan's plan was to save the Republic by going to war then going away (cf wikipedia articles) then Sion and Nihilus (not the true Sith, according to her, just vandals, like Malak), then she would have them killed. She was never afraid of them as such.