The answer to this question can be found in Chapter Twenty of this excellent novel. After Kit's near escape during her trial when fortunately she was proven to not be a witch, thanks to Nat's intervention, Kit has realised some fundamental things about herself and also about William Ashby and how different they are as characters. William's decision to not side with Hannah, Prudence and Kit during their time of need has taken away all respect that Kit has for him, and she realises now that she would never be truly happy being married to him. Note what she says to him:
"'Tis no use, William," she said now. "You and I would always be uneasy, all of our lives. We would always be hoping for the other one to be different, and always being disappointed when it didn't happen. No matter how hard I tried, I know I could never care about the things that seem so important to you."
Kit has obviously now learned the lesson that Hannah tried to teach her before. That escape from a situation that you don't like can often lead to a worse kind of servitude. Whilst marriage to William would give her the social status that she craves, she would never be happy being married to William as they think very differently.
william did not attend kit when she needed help but Nat did so she leaves william and marries Nat