First off, I don't think that Nihilus is the Exile's dark half. From my understanding, the exile was extremely good at establishing Force bonds with people she was around for prolonged periods of time, and at Malachor, everyone of the people she was connected too either fell to the Dark Side or was slaughtered, causing so much pain in the Force that the exile cut herself off from the Force in reaction, or it would have overwhelmed and destroyed her- rather than her dark self simply splitting away.
Also, the fatal flaw: Nihilus is a male, while the canon Exile is a WOMAN.
You could argue that the essence of a person has no gender, but lucasarts would not confuse people like that.
I apologize in advance if this has already been suggested, but this thread was getting a little mind numbing to read all the way through.
So here is my thought: The Exile had an affinity for connecting to people through the Force. Why? Well, perhaps it was simply something in her personally, but perhaps it came about from being introduced to the Force by someone who had the same affinity.
Perhaps Darth Nihilus was what became of the Exile's master. This would certainly explain their supposed 'connection'.
The bond that forms between a master and apprentice is supposedly stronger than any other- (I believe Bastila even mentions that in passing), so, in theory, when the Exile was forced to retreat from the Force, it would have left not only a wound in the Force, but an extreme emptiness in the one most connected to her- an emptiness that could quickly turn to hunger.
"Everything I tell you is a lie. Every question I ask you is a trick. You will find no truth in me."
―Vergere to Jacen Solo