I agree with everything you say about Fanny, but I take a less charitable view of Sir Thomas.

Perhaps this is a minor masterpiece - the writing is certainly effective, so much so that I think it one of the most disturbing scenes in JA's works. BarbaraB said - "The words feel almost physical". Just so! I find Sir Thomas' tirade quite distressing to read. It begins:

Sir Thomas came towards the table where she sat in trembling wretchedness, and with a good deal of cold sternness, said......

So we start with a girl whom Sir Thomas knows to be timid, in a state of trembling wretchedness.
Then he goes on, and on, and on. He begins in tones of cold sternness but by the end of it he is angry. By this time Fanny is crying bitterly, her heart almost broken. She says she is sorry, through her tears, but Sir Thomas has to have the last word and carries on. Fanny makes a huge effort; she protests that she would be miserable and is overwhelmed by another burst of weeping.

Does Sir Thomas give any consideration to the idea that Fanny might have a right to her own opinion on such a matter or that she might refuse to marry a man she does not like? Does he feel any remorse at causing her such distress? Not a bit of it! He watches her weeping, reflects that with a bit more pressure he may still get the outcome he wants. This cheers him up, and only then does he speak to her in tones of less anger!

Sir Thomas may be behaving as a gentleman in that he does not yell or threaten physical violence, but his cold control and detachment as he reduces a timid young woman to such wretchedness is chilling. It is every bit as unkind as Mrs Norris' worst scoldings, and more frightening because he has more power.

Two aspects of what Sir Thomas says in this passage make me very angry. He berates Fanny for daring to think for herself, as if she has no right to independent thought. He also seems to think that she has no right to refuse an offer of marriage simply because she does not like the man and knows she would be miserable. To me these ideas are offensive and disgusting beyond all common offence. Sir Thomas, reflecting the assumptions of his society, demonstrates here what is fundamentally wrong with patriarchy!