"He did it for Kaoruko... didn't he?"
It sounds cheesy, but Rintaro's love for Kaoruko really did make a big impression on Ayu. Simple, but effective.
This is truly an "everything I believed about Chidori was a lie" moment... and the worldview shaped by her teachers has collapsed with one reality check event. She had a coping mechanism built upon the lies she heard about Chidori, and the final straw was learning that someone from there could actually be smart. Smarter than her or another Kikyo girl, even.
Their kindness is killing her (old self) and our good boy Rintaro is here to deal the finishing blow; (so she can become one of their friends? or so I hope...)