I don't think it's her self loathing that she thinks is impure. It's her desire for women, specifically Kanon in this case. She thinks it's impure to want her, to be gay. It's internalized homophobia. It's been her character from the first chapter.
You're right, but I think we're essentially arguing the same thing. They go hand in hand. Her self-loathing is rooted in thinking her desire for women, specifically Kanon, is impure.
I say this because during the discussion of being pure and impure Saki states "Someone like me, in this state, isn't worthy of you Kanon." That phrase "in this state" is key. She's distinguishing between what she
is and what she's
going through. Being gay is a state of being. Who you are, and not something you can change easily. Self-loathing is a mental state. A condition you're in, something that can be worked through or healed. Unless Saki plans to stop being gay, and there's no sign she will, "this state" cannot refer to her queerness when she says she isn't worthy.
Bear in mind Saki says this after they've already confessed their love to each other. Kanon already knows she's into women. Thus, from my interpretation, the impurity she's clinging to isn't just that she likes girls. It's everything that came with hiding it for so long. The walls she put up towards Mashiro, the overthinking, the bitterness. All of it piled up into this version of herself she doesn't think deserves love, even when it's right in front of her saying otherwise. The version of herself that is consumed by negativity, that cannot be open about who she is, that hates herself for it, that is what is not worthy of Kanon. This is where the impurity truly lies. Not solely in her identity, but in the shame she carries for it.