I don't think it was fear because if you remember Khushi remembers the scene where Arnav slapped Shyam and declared Khushi to be one of the two most important people in his life.
I think it was nervousness, helplessness and sadness.
Nervous because their entire relationship has just changed and she doesn't know how to be around him. She knows she wants him near her, but she doesn't know if he needs space or what. You see, after he stopped her from leaving, she walks slowly towards him, but when she realizes that he wants her to be close to him, she rushed into a hug with him.
Helplessness and sadness because she can't do anything to take away his pain of being separated from Anjali after everything that has happened. He supported her and that caused Anjali to call him Arnav and ask to be left alone.