He has many reasons to hate her. First as you said he knows Samrat went missing because of Pakhi. She has betrayed his cousin brother. He also likes Sai immensely because she is the only one who supported him. Even his own parents, wife and brother didn't support him but Sai was a stranger. No wonder he has started to like her. He very well knows she is the right person for Virat. He also knows that most of the drama happens because of Pakhi.