Rin's always come across as pretty self-absorbed to me, so her callousness with Molly seems congruent with that. She's plenty happy to make demands of and set boundaries on other people, to burden other people with her problems, but when has she done something scary, made any personal sacrifice, or stood up for someone other than herself? She may well be self-aware of this, hence the self-deprecating, self-loathing nature, but she also doesn't take any actions to contradict this nature either. She just keeps on going with the flow of whatever her emotions are telling her this day. Her story has been all about self-discovery, which is really just a euphemism for narcissism.
What is Molly in the confession scene to her? Someone scared and confused, confronting feelings they don't fully understand... or a dangerous, unsanitary creep and potential sexual assailant? There's an assumption that she would be sympathetic and understanding given the parallels, but what if she's just... kind of a shitty person? It's flattering to think that neurotic tendencies will at least give you a better perspective, make you more empathetic, but it could just make you treat everyone like an object.
Rin treated Molly just as she treats Sensei, Chika, and Otoha. The only difference is valence.
...or I suppose you can chalk it all up to the author dun goofed.