She just wished for witches to be gone, not the whole system. However, I think she made the perfect choice. If she wished the whole system away, the whole crew would've had nothing to do with eachother, and that would be a completely boring and bad timeline. Also, society would be broken too. Past wishes made the foundation for their everyday life. Everyone was saved. Sayaka just isn't with everyone else. I like to think of her as being with Madoka.
Its better than them not knowing eachother at all. I was hoping for a Kyouko Sayaka end too.;;