This question is a bit vague. Without a more specific story reference, I am going to have to make an educated guess. I also think that Kit chooses to do both her duty and remain loyal to Hannah Tupper. In the final third of the story, a terrible fever strikes the town. Even Kit gets sick, and Mercy is especially sick. Being a superstitious town, the people decide that they need a scapegoat to blame the illness on. They believe that Hannah Tupper and her strange ways are to blame. They think she is a witch, so they form a mob with the intention of burning her house down. At this point, Kit chooses Hannah Tupper. Kit rushes out to warn Hannah of the coming danger.
She would have to get to Hannah. No matter what happened, she could not stay here and leave Hannah to face that mob alone. If she could get there in time to warn her—that was as far as she could see just now.
Nat also shows up, and he spirits Hannah away to his grandmother's house. He offers to give Kit sanctuary as well; however, Kit chooses her duty to Mercy and the family:
"Or you can go on to the West Indies with us."
Barbados! The tears sprang to her eyes. "I can't, Nat. I have to stay here."
The concern in his eyes hardened to awareness. "Of course," he said courteously. "I forgot. You're going to be married."
"'Tis Mercy," she stammered. "She's terribly ill. I couldn't go, I just couldn't, not knowing—"