If Sir Thomas’ opinion of Fanny is as you suggest then it is very surprising that he gives a ball in honor of her and William? Also it is rather unusual that he always gratified her greatest wish of being able to invite William to MP at every opportunity. Is there some evidence his approval of the match with Henry is because he wishes to get rid of Fanny? I feel the description of “mouse to be ignored” is not supported by the text:

Sir Thomas was at that moment looking round him, and saying, “But where is Fanny? Why do not I see my little Fanny?”—and on perceiving her, came forward with a kindness which astonished and penetrated her, calling her his dear Fanny, kissing her affectionately, and observing with decided pleasure how much she was grown! (19)

William’s desire of seeing Fanny dance made more than a momentary impression on his uncle… He remained steadily inclined to gratify so amiable a feeling; to gratify anybody else who might wish to see Fanny dance… “…the dance which I think of giving at Mansfield will be for their cousins.” (26)

Sir Thomas himself was watching her progress down the dance with much complacency; he was proud of his niece; and without attributing all her personal beauty, as Mrs. Norris seemed to do, to her transplantation to Mansfield, he was pleased with himself for having supplied everything else: education and manners she owed to him. (28)

Sir Thomas immediately improved this compliment by adding, “Very true. We shew Fanny what a good girl we think her by praising her to her face, she is now a very valuable companion. If we have been kind to her, she is now quite as necessary to us.” (28)

Mrs. Norris had not discernment enough to perceive, either now, or at any other time, to what degree he thought well of his niece, or how very far he was from wishing to have his own children’s merits set off by the depreciation of hers. (32)