Does Sir Thomas Bertram Punish Fanny for Refusing Crawford?

In an often misunderstood novel, Sir Thomas Bertram's reaction to Fanny's refusal of Crawford's declaration of love is an often misunderstood element. That Fanny does refuse is easily understood by readers as it is made quite clear by Austen's narrator: "she did not love him, could not love him, was sure she never should love him;...." What is less easily understood is the reaction Sir Thomas has to Fanny's refusal.We are told that his first reaction was disappointment though this was followed speedily by hopeful confidence in Crawford's plan of perseverance and constancy. We are told that Sir Thomas so thoroughly endorsed Crawford's intentions and plans that there was nothing "omitted, on his side, of civility, compliment, or kindness, that might assist [Crawford's] plan."
{Sir Thomas's] first feeling was disappointment: he had hoped better things; he had thought that an hour's entreaty from a young man like Crawford could not have worked so little change on a gentle-tempered girl like Fanny; but there was speedy comfort in the determined views and sanguine perseverance of the lover; and when seeing such confidence of success in the principal, Sir Thomas was soon able to depend on it himself. (XXXIII - 33)
We are told that when he brought the subject up with Fanny, Sir Thomas's response to her anguished entreaties of regret mixed awkwardly with conviction was that she should have "nothing to fear, or to be agitated about" since he most assuredly would not try to persuade her "to marry against [her] inclinations." He avowed that her " happiness and advantage" were all that he "had in view." While he did tell her that Crawford would continue to socialize and that her only burden would be to try to proceed with equanimity under Crawford's "endeavors to convince" her of their suitability, Crawford was informed that "[h]e proceeds at his own risk.""You will have nothing to fear, or to be agitated about. You cannot suppose me capable of trying to persuade you to marry against your inclinations. Your happiness and advantage are all that I have in view, and nothing is required of you but to bear with Mr. Crawford's endeavours to convince you that they may not be incompatible with his. He proceeds at his own risk. You are on safe ground. I have engaged for your seeing him [with the rest of us] whenever he calls, as you might have done had nothing of this sort occurred." (XXXIII - 33)
Sir Thomas is inspired by William's (Fanny midshipman brother's) recent promotion to lieutenant to come up with a scheme that might have several benefits. He does not enact the scheme without first getting Edmund's opinion and consent, since Edmund seems to understand Fanny in a way that Sir Thomas does not. He hopes by the scheme to fulfill William's wish that Fanny might see his new uniform; to reunite for a brief time Fanny with her Portsmouth family; and to encourage Fanny to more highly value the attention and admiration she receives from Crawford, especially as it would contrast so starkly with the neglect and deprivation all expect her to experience with her impoverished and unrefined family.This scheme was that she should accompany her brother back to Portsmouth, and spend a little time with her own family. It had occurred to Sir Thomas, in one of his dignified musings, as a right and desirable measure; but before he absolutely made up his mind, he consulted his son. Edmund considered it every way, and saw nothing but what was right. The thing was good in itself, and could not be done at a better time;.... (XXXVII - 37)
What the text clearly tells us is that Fanny did not fall out of favor with Sir Thomas and that Sir Thomas did not punish Fanny by sending her away to Portsmouth. What Sir Thomas in fact did was to respect Fanny, uphold her moral position as far as he understood it, and to combine the benefit of a family reunion with an object lesson so that her, as he supposed, youthful delicacies might be redirected to more mature sentiments that included practicality and sense.