Oh, I think it was very well done indeed. The OP doesn't take into account that Emma has in the past days had her world and her self-view very shaken - Beckinsale handles admirably, I think, the dropping of Emma's self-assurance, her acknowleding her less than admirable conduct, her failures of observation with a touching hesitance - the mask is off, she is just a very young woman, uncertain of herself for the first time in many years.
For her to be a little stunned by Mr. Knightley's declaration of love is very much more natural, under these circumstances, than a simple - "oh, it's all OK now!" about face. Austen shows us, in other novels, that she understands this - in "Pride & Prejudice," after engaging herself to Mr. Darcy, Elizabeth Bennet "rather knew herself to be happy than felt herself so." Or very close to that wording.
It's also prhaps worth noting that this adaptation, much like the book, isn't really a romance. The 1996 Miramax film and the 2009 BBC mini-series treat it so, but look at the realities - Emma has found her happiness, not with the dashing, romantic Frank Churchill, but with the steady Mr. Knightley, who is already family to her. Austen explicitly twins Emma's and Harriet's alliances; the contrast is Jane Fairfax and Frank Churchill - in the former two alliances, it is the husband who provides the steadiness and stability, in the latter, it will be the wife who does so. The romantic hero, then, is presented, to his disadvantage, by comparison with the two farmers, Mr. Knightley and Robert Martin (yes, they are on vastly different levels of society, but they are both farmers, grounded in the realities of the land and the seasons).
I absolutely love this film; I do also love the 2009 mini-series despite the unevenness of the production and the rather uneasy "modernizations;" while not as faithful, it does provide a number of illuminating insights to some aspects of the characters that get short shrift elsewhere. I don't much care for the 1996 Paltrow film, although it is well made and well acted. I don't believe Douglas McGrath truly understands the book at all, alas.
Oh, right. So, she secretly trained a flock of sandflies.