Because Lucia does not conform to the pure, chaste idea of womanhood, she is called a "whore " and a "witch." She is pregnant with Takesure's child but has also been having sex with Jeremiah, her sister's husband.
Lucia uses her wiles to get herself away from the homestead with Jeremiah and Takesure. She is six months pregnant when she gets to the mission, with the declared purpose of helping her sister give birth. Lucia has her own sense of right and wrong, she has a moral code that exists separate from tradition. Part of this code is helping her sister when others do not. I think we see the hypocrisy of tradition and the sincerity found in people, like Lucia, who are looked down upon.