The other Jedi would be affected in different ways. Some might see her as a traitor and become more strict in their views, while others might secretly sympathize with her. It could create a divide within the Order in the fanfiction.
For his friends, it could be a huge blow. They might feel abandoned and worried about his safety. For example, Annabeth could be extremely distraught, constantly worried about Percy's well - being. Some of the younger campers who looked up to Percy might lose their sense of hope and inspiration. They may feel less secure without him around.
His friends might feel sad and abandoned. For example, Hermione and Ron could be heartbroken at first, missing their best friend and wondering if they could have done something to make him stay.
One possible reason could be disillusionment. In some crossovers, she might see the Jedi Order's flaws more clearly when exposed to different cultures or ideologies from the crossover elements. For example, if it's a crossover with a more individualistic society, she may start to question the Jedi's collectivist approach.
For Tony Stark, it could be a blow to his ego. He might see Peter's departure as a sign of failure in his mentorship. He could also start to question his own actions and decisions that led to Peter leaving.
Arya might be inspired to go after him. In fanfiction, she could see his departure as a call to adventure herself. She might feel that there are things out there that she can learn from Jon or things she can do to help him. His leaving could be a catalyst for her own journey outside of Winterfell.
For Hermione, it could be a huge loss. She might feel abandoned and try to find ways to bring him back. Ron, on the other hand, might be angry at first but then also miss his best friend terribly.
Her departure could create a power vacuum in certain areas. Since she was a powerful Jedi, there might be regions she was protecting that now become vulnerable to the dark side or other threats.
The town of Beacon Hills itself might be affected. Stiles was always in the middle of things, helping to solve supernatural mysteries. Without him, there could be an increase in unexplained events. And some of the townspeople who knew Stiles, like Sheriff Stilinski, would be deeply affected on a personal level, with the sheriff possibly becoming more overprotective of the remaining youth in town.
For Sakura, it could be a huge emotional blow. She might feel abandoned and be motivated to become stronger herself to bring them back. Also, she might have to step up in their absence and take on more responsibilities in the village.
She could have Clone Troopers as her allies. Some of them might have defected with her and believe in her innocence. They could provide military support and loyalty.