I agree Emma would be rendering justice by giving up her suspicions of a romantic entanglement between Jane and Mr. Dixon but unfortunately Emma does not believe indulging in these suspicions is unjust. On the other hand Emma knows her treatment of Jane Fairfax has never been what it ought to be:

Emma was sorry to have to pay civilities to a person she did not like through three long months! to be always doing more than she wished, and less than she ought! (20)

Emma knows the basis of her dislike of Jane is not fair:

It was a dislike so little just -- every imputed fault was so magnified by fancy, that she never saw Jane Fairfax the first time after any considerable absence, without feeling that she had injured her… (20)

Emma feels guilty for the injuries, “past prejudices and errors” (20), she has inflicted on Jane by neglect and depreciating Jane’s appearance and manners for the last two years:

In short, she sat, during the first visit, looking at Jane Fairfax with twofold complacency; the sense of pleasure and the sense of rendering justice, and was determining that she would dislike her no longer. (20)

Emma is rendering justice by recognizing Jane deserves her civility and attention for personal merit (the much appreciated elegance) and her situation both real and imagined whereas in the past she failed to do so. Essentially Emma is protecting Jane from her own prejudices against her by admitting her worth and intending to act accordingly.