It seems “No, no, no!” plus the fact Fanny ‘had burst away from him’ and then ‘rushed out at an opposite door’ (31) ought to be enough to at least suggest to Henry she does not want him. I think he is too vain to believe Fanny’s reluctance is anything other than modesty and unfortunately her demeanor works with this interpretation. Sir Thomas may have been a fan of John Gregory who gave advice on female behavior in A Father’s Legacy to His Daughter (1774) or at least of ideals of the same nature. One advice was from the portion titled Conduct and Behavior and fits Fanny’s reaction to Henry’s proposal very well:

One of the chief beauties in a female character is that modest reserve, that retiring delicacy, which avoids the public eye, and is disconcerted when at the gaze of admiration…

Henry probably described Fanny’s reaction to Sir Thomas as modest and embarrassed and they both perceived it to be ‘as much encouragement to proceed as a well–judging young woman could permit herself to give’ (32). Of course Fanny was modest and embarrassed but also disbelieving. It also seems there was an established mode in how to refuse an offer of marriage and perhaps Fanny’s not following it adds to why Henry does not accept her rejection. Lizzy Bennet (P&P) rejects two proposals both of which she attempts to answer in what appears to be a kind of form civility designed reject and compliment at the same time—express sensibility of the honor bestowed and gratitude for it and then gently refuse:

"You are too hasty, sir," she cried. "You forget that I have made no answer. Let me do it without farther loss of time. Accept my thanks for the compliment you are paying me. I am very sensible of the honour of your proposals, but it is impossible for me to do otherwise than decline them." (P&P, 19)

Of course Lizzy could not quite do it with Darcy:

In spite of her deeply rooted dislike she could not be insensible to the compliment of such a man's affection… "In such cases as this, it is, I believe, the established mode to express a sense of obligation for the sentiments avowed, however unequally they may be returned. It is natural that obligation should be felt, and if I could feel gratitude, I would now thank you. But I cannot… (P&P, 34)

I can see why nothing of this sort is in Fanny’s response to Henry. Before he proposed she was already exceedingly distressed feeling his trifling and gallantry was ‘treating her improperly and unworthily’ (32) and add to that she had already ‘twice drawn back her hand, and twice attempted in vain to turn away from him’ (32). Fanny desperately wished to escape but her feelings of gratitude for his efforts on William’s behalf made it difficult to extract herself. I also feel it is interesting Henry was not surprised at Fanny’s reaction to his proposal. He believed it was evitable because of her nature:

It was no time for farther assurances or entreaty, though to part with her at a moment when her modesty alone seemed, to his sanguine and preassured mind, to stand in the way of the happiness he sought, was a cruel necessity. (31)

Henry expected Fanny’s modesty to delay his happiness. For a man who delights in trifling with the fiancées of other men Fanny’s ‘modest and elegant mind’ (30) is all important because that is why he can trust her not to betray him, is willing to risk his happiness and why she is ‘Heaven’s last best gift’ (4). Henry’s vicious propensities make him a man particularly aware of Fanny’s value:

…her manners [Fanny’s] were the mirror of her own modest and elegant mind. Nor was this all. Henry Crawford had too much sense not to feel the worth of good principles in a wife, though he was too little accustomed to serious reflection to know them by their proper name; but when he talked of her having such a steadiness and regularity of conduct, such a high notion of honour, and such an observance of decorum as might warrant any man in the fullest dependence on her faith and integrity, he expressed what was inspired by the knowledge of her being well principled and religious. (30)

A little more on Sir Thomas’ view of Fanny—I feel his view of Fanny is colored by his ideas of what is correct female conduct and he is prone to see people in the best light (according to him) as well. I guess it could also be described as a lack of imagination. I think when Fanny says “If it were possible for me to do otherwise” (32) rather than enforcing her desire to oblige him but explaining that she inherently cannot because “I am so perfectly convinced that I could never make him happy, and that I should be miserable myself” (32) it instead invites him to believe she is persuadable about Henry.