What is up with Mrs. Thornton? An abundance of caution. She does love Captain Lee, BUT she also sees their professional situation and also the deep scarring he has after 23 years of hard military service. They have only known each other for seven months, with three months of all-out crisis at their shared place of work. He has literally and personally disposed of FIVE of her immediate superiors, who just happened to have been corrupt commissioners of police, in that three months. She knows Captain Lee is a dangerous man, in addition to being a perfect gentleman who is kindly disposed toward all the good women around him -- that runs in the family, given that he has a REAL 19th-century uncle whose orders disposed of 100,000+ men's lives in defense of the desire for PERPETUAL slavery under the Confederacy. So: Mrs. Thornton is not letting her heart run away with her head!