Rin has been trying to get Aoki to see her as a woman since the beginning of the manga series. This prank was her most successful try, over the phone she was invisible and so she could converse with Aoki as an equal, under false pretenses.
Without getting into right and wrong, the way Rin feels seems quite deep and genuine. This series is in a way the complete opposite of Nabokov's Lolita -- in that book Humbert's feelings are completely genuine, but Lolita is a completely inappropriate object for his affection, wrong in 1000 ways. In this manga, both Rin and Aoki are honest and affectionate people. It does make you wish that they could solve their problems and get together sooner or later.
One of the most beautiful frames of the series shows Rin's despair at how Aoki sees her. It's at the end of Chapter 20.
Manga Fox: Kodomo no Jikan Vol.03 Ch.020 Online Manga Scans