It could also be due to a sense of confusion. Naruto suddenly finds himself in this unexpected situation. He doesn't know how to deal with it and feels that running away is the easiest way at the moment to escape from all the chaos and figure things out on his own.
Sasuke could be one of the people to help. Despite their past differences, Sasuke has a deep connection with Naruto. He might be able to understand Naruto's situation and offer his protection and support.
It could be that Naruto discovers something about the nature of his pregnancy that scares him. For example, he might find out that the child has some sort of special power that could put it in danger. So he runs away to figure out how to handle the situation without endangering the village or the child. He might seek out a hermit or an old sage to get advice on what to do.
One possible scenario in this kind of fanfiction could be that Ginny discovers she's pregnant at a very inconvenient time. For example, there might be some dark forces rising again in the wizarding world, and she fears for the safety of her child. So she decides to run away to a secluded place, perhaps a small cottage in the countryside that she discovers through some old family connections. This would also give the author a chance to explore Ginny's maternal instincts and her ability to fend for herself.
Maybe he's running away from the pressure in the village. There are always high expectations on him, and he might feel suffocated and need some time alone to figure things out.
One consequence could be that his friends worry about him a great deal. They might go on a search for him, which could put them in danger as well. After all, they care about Naruto deeply and won't just let him disappear without trying to find him.
One possible theme could be self - discovery. Harry, being in such a difficult situation, might go on a journey to find out more about himself and what he truly wants. Another theme could be facing consequences. Running away while pregnant has its own set of challenges and consequences that he would have to deal with.
One possibility could be that Stiles runs away because he's afraid of the reactions from his friends and family. Maybe he thinks they'll be disappointed or angry. He might go to a place where no one knows him to start a new life for himself and his unborn child.
In this fanfiction, it could be that Lucy is part of a society with strict rules about pregnancy out of wedlock. She runs away pregnant to avoid the shame and punishment that would come her way. As she runs, she might meet other outcasts who support her. She then has to figure out how to survive, find medical care for her pregnancy, and create a future for herself and her baby.
It could be Ron. Maybe they had a falling out or some sort of misunderstanding during their relationship, and Hermione runs away when she discovers she's pregnant. Another possibility is that it's a new character, someone she met during one of her adventures or studies. This new character could be from a different magical culture, and their relationship was a secret.