First, I don't buy it. He is not the father. It's too sudden and lacks of foreshadowing. If he really IS, the glasses black hair woman teacher would already tell Itsuki about him, CONSIDERING They meet up directly.
Second, this is Negi I am talking about. He is not dumb enough to introduce a bombshell out of nowhere just for the sake of the plot. At least that's what I thought seeing the previous 108 chapters which are consistent.
Third, Itsuki is a rare case between the quints. She is the only girl that doesn't show obvious romantic feelings with Fuutarou. Her relationship to him is more like a trusted partner, guardian, and what Negi showed "A substitute father". Of course this "substitute father" will progress when there is an arc where she is revealed that Fuutarou is regarded more in her heart than she previously perceive. A combination between a little mystery of father's figure , Itsuki's dilemma on her dream, and Fuutarou's convincing her path would be a good wrap up.
Tl;dr. He is not her father. This arc is about Itsuki. Maybe we'll get some reveal in the future, but not that rushed