Maybe she has some unresolved issues from her past, like her unrequited love for Sasuke that still lingers in the back of her mind. This could make her question her relationship with Naruto and lead to her leaving.
It could also be that she is forced to abandon them due to some external threat. For example, if an enemy targets her family and she believes that leaving them is the only way to keep them safe from harm.
One possible reason could be his sense of duty. Sasuke has always been driven by his goals for the village or his personal vendettas. Maybe he feels that his mission is more important than staying with Sakura and their unborn child, believing that his actions are for a greater good that will ultimately protect them as well.
One possible reason could be that Sakura realizes she has different goals or values that are not compatible with being around Naruto. Maybe she discovers a new path in life that doesn't involve him, such as focusing on her own medical ninja career without Naruto's chaotic lifestyle interfering.
She could also try to find Sasuke and clear up any misunderstandings. Sakura is not one to give up easily, especially when it comes to someone she loves. She might set out on a journey to find him, believing that she can bring him back and make him realize the importance of their family.
One possible reason could be extreme jealousy. Sakura might be so blindly in love with Sasuke that she sees Naruto as a threat to Sasuke's attention or her relationship with Sasuke. Maybe she thinks Naruto is getting in the way of Sasuke's return to the village or her attempts to win Sasuke back.
One possible reason could be a misunderstanding. Maybe she was misled by false information about Naruto being a threat to the village. Another reason might be that she was under some kind of mind control. In some fanfictions, dark magic or evil entities can take over a character's mind and make them act out of character.
Perhaps there was some sort of dark influence at play. In the world of Naruto, there are often dark forces and genjutsu (illusion techniques). It's possible that Naruto was under the influence of a genjutsu that made him see Sakura as a threat, so he punched her in self - defense without realizing it was an illusion.
He could become very determined to find out why Sakura left and try to win her back. Naruto is known for his perseverance, and he wouldn't give up easily on his family. He might also start to question his own actions and wonder if he could have done something differently to prevent this.
One possible reason could be that she sacrifices herself to save Naruto from a powerful enemy. In the heat of battle, she might put herself in harm's way to ensure Naruto's survival.
One possible reason could be that she might be facing some sort of internal conflict. Maybe she has some unresolved issues from her past that resurface and make her feel like she can't be a part of Percy and their daughter's life. It could also be that she feels pressured by some external force, like a new threat in the world of the fanfiction that she believes she has to face alone and in doing so, she has to leave them behind.
Perhaps Sakura is in a situation where she thinks Naruto's actions are endangering the village or their friends. In the Naruto universe, they often face difficult choices and she might believe that Naruto's continued existence is a greater threat than his death at that moment. It could also be that she has been poisoned or affected by some sort of jutsu that clouds her judgment and makes her say such a cruel thing.