Why do I have the feeling that this turn of events will psyche Shounen out and he'll fail his exams because he's going to be too hung up over what happened this chapter and how he was implicitly (but not outright) rejected.
Onee-san likes him back. But she is insecure and legitimately worried that she will cause him to not study for his exams and not dedicate himself. She is trying to push him away because she knows no better. That is the only way she could be sure that he won’t get himself be distracted by her.
TL;DR: She cares so much about him that she is pushing him back so Shounen doesn’t fuck up his education for her. Why? Insecurity.