The root of Saki's unease has always been her internalized homophobia and beating herself up over her clearly sexual desires towards women. She's known she's sexually attracted to women for a long time and somehow internalized it as something "abnormal" and "impure".
"Dark Saki" represents the superego in psychology. It reflects the internalization of cultural rules and everything "authorities" (whether parents, school, friends, TV, media, whatever) have hammered into her brain. It's not something you get rid of on a snap. It obviously takes considerable effort on Saki's part to voice something so deeply buried, to the point of making her cry.
She wants to bare herself to Kanon and dismiss Dark Saki. And that can only be done by laying down all her "secrets". That's just how much she loves Kanon.
It's obviously what Kuzushiro planned all along, since chapter 1 and that's rare enough these days to have a mangaka planning a story for more than 3 volumes in advance.