Because he decided to stay for her.
Because she didn't want him to leave her.
ANYA: Oh, thank goodness. (puts it back on)
GILES: (comes out from behind counter) I'm so sorry, dear.
ANYA: No. Rupy, I'm sorry. You were right. That was the wrong book.
GILES: Oh ... um ... (stutters, removes his glasses) Yes, it was. But I'm, I'm still sorry.
ANYA: Don't leave me.
GILES: Oh, Anya.