I have no doubt he had fatherly feelings toward Faith. IMO I think its obvious he did. As he finds the mess she and Buffy left behind, he mutters to himself "She'll be ok. She'll be ok." If he had no feelings, would he not care? Then as he is in the hospital with her, he strokes her hair, an obvious sign of affection. After that, he tries to kill Buffy, trying to get revenge for hurting Faith. A father who is in an unstable crazy condition who just had their daughter put into a most likely permanent coma by another girl who will recover, would most likely do something similar. Lastly, Buffy tricks him into chasing her by holding up the knife and saying "It slipped into her like butter." If he had no feelings, he would have brushed that off. If he did not care about Faith, her being nearly killed by Buffy would have not affected him at all. He would have been merely losing one of his pawns, and he's never seemed to care about them in the past. That comment provoked him though and made him angry.