Negan may have lied about Ginny's father to make her angry enough to leave with the Marshal. Upon reuniting in finale, Ginny refuses to leave Negan. When Ginny tries to speak for the first time, Negan shuts her down by admitting he murdered her father. He claims he kept her around to pay off a personal debt. However, this seems like it's a spur-of-the-moment admission. Perhaps Negan needs to come up with a lie that can convince Ginny to let go of him completely.
As seen throughout , Ginny is too stubborn to live in a community without Negan. She even leaves the safe haven to find Negan in New York. In a , where Maggie betrays him to get back Hershel, Negan realizes that Ginny shouldn't be a part of his mess. Negan knows that Maggie intends to hand him to the enemies. As such, he makes the difficult decision to push Ginny away. He targets what hurts her most — the trauma of her father's unexpected death — so that she'll be too enraged to care about him anymore.
Negan understands how dangerous the world is, especially with people like the Dama. , and he's able to bring out his villainous tendencies from the Savior war. Ginny being around such enemies would do more harm than good. It's possible the Croat would torture her if he ever got the chance. By pushing Ginny away, Negan cuts the emotional ties between them. Lying about killing her father is the best way to remove Ginny's attachment before she becomes too dependent on him, something that was already starting to happen by the end of season 1.
has proven through the years that emotional attachments never end well. Negan, a hardened survivor who makes difficult choices to protect himself, may not want the responsibility of looking after a child. He likely doesn't want to experience the potential pain of losing her. Negan's done this before. He sent his wife, Annie, away because he wasn't able to protect her. It's possible he wants to give Ginny the same chance of survival. That's why season 2 will likely reveal that Negan lied about killing Ginny's father. Of course, audiences will need to wait for the next outing to know for sure.