Her refusal of Robert Martin's marriage proposal is a material point in changing Mr. Knightley's judgment of Harriet. He had not expected that. But when she did refuse, he judged her differently after learning this fact. I do not see this as inconsistency, but as adjusting his judgment to take into account a relevant new fact.

Mr. Knightley's sense of Robert Martin and Harriet was right to begin with. The only reason that he was wrong in fact, i.e. the only reason that Harriet did refuse Robert Martin, is because Emma manipulated her, which, unfortunately, wasn't very difficult for her to do -- which is why Mr. Knightley objected so strongly to the friendship between Emma and Harriet in the first place -- and he was right to do so.

Mr. Knightley is not wrong in judging Harriet to be a simpleton for refusing Robert Martin, who really loves her. And I think that Mr. Knightley thought well enough of Robert Martin to suppose that he would not propose to a young lady unless he had some basis for believing her to return his affection.

And Harriet did return Mr. Martin's affection, and IMO never really loved anyone else. Left alone, as she would have been if Mr. Knightley had had his way in the matter, her natural sense of what was good for her was correct.