Well the Sith at that point were killing all the Jedi right? At one point the Exile was pointed out as the last of the Jedi to the Sith by Atris.. And the Exile is special to Kreia, as we all know, so she would not allow the others to kill her. Sion and Nihilus probably saw that as weakness and exiled her... And yes, there was no scene intended to show the dispute, this cutscene can be unlocked early in the game and therefore couldn't reveal too much information.. that's why they cut the other line too, I think, it would have given away too much too soon.
Oh and one small note to finally correct this big misconception: Atris being the final boss was never intended, it's a misconception due to Atris speaking some of Kreia's lines on Malachor, but that was probably because of a confusion at Obsidian, since both voice actresses played the character 'Darth Traya'.