I feel Sir Thomas does believe Fanny has a right to independent thought and to refuse Henry.

Sir Thomas, in my opinion, does not berate Fanny for thinking for herself what he says is ‘that you can and will decide for yourself, without any consideration or deference for those who have surely some right to guide you, without even asking their advice’ (32) which is not quite the same. He thinks Fanny has made a decision to throw away as good an offer as she may ever receive, one he would have gladly approved for either of his daughters, based simply on romantic notions without considering the worth of the gentleman or duty to those who have her best interest at heart:

You think only of yourself, and because you do not feel for Mr. Crawford exactly what a young heated fancy imagines to be necessary for happiness, you resolve to refuse him at once, without wishing even for a little time to consider of it, a little more time for cool consideration, and for really examining your own inclinations; and are, in a wild fit of folly, throwing away from you such an opportunity of being settled in life, eligibly, honourably, nobly settled, as will, probably, never occur to you again. (32)

I think there are several reasons Sir Thomas does not accept Fanny’s stance that she ‘cannot like him… well enough to marry him’ (31). He does not know Fanny well enough to understand her opinion of Henry was not formed quickly or frivolously. I do not blame Fanny for not explaining her opinion of Henry but by not doing so her opinion of him hardly seems credible. His observations do not give any support to her position either so he concludes she does not know Henry well enough to positively determine she dislikes him and would be miserable in the marriage. Of course Sir Thomas, as he has so often been, is wrong.

Sir Thomas believes Fanny has a right to refuse a man because she does not like him or any other reason. He tells her:

‘You must give him [Mr. Crawford] your own answer: we cannot expect him to be satisfied with less; and you only can explain to him the grounds of that misconception of your sentiments, which, unfortunately for himself, he certainly has imbibed’ (32)