I think as punishment for wishing “to see Emma in love, and in some doubt of a return” (5) it is very fit that Mr. Knightley suffer the same fate and he did—he was in love with Emma and had little hope of a return because he thought her affections were engaged elsewhere. Why should not Mr. Knightley advise Emma? It is not as if she has not needed it and there is no one else who will provide it. Per the narrator:

“Mr. Knightley, in fact, was one of the few people who could see faults in Emma Woodhouse, and the only one who ever told her of them…” (1)

Mr. Woodhouse sees no wrong in Emma, Mrs. Weston is too gentle, “For shame, Emma! Do not mimic her [Miss Bates]. You divert me against my conscience” (26) and Mr. John Knightley lives in town or he might help Emma with good advise such as this more often:

"Mr. Elton in love with me! What an idea!"

"I do not say it is so; but you will do well to consider whether it is so or not, and to regulate your behaviour accordingly. I think your manners to him encouraging. I speak as a friend, Emma. You had better look about you, and ascertain what you do, and what you mean to do."

"I thank you; but I assure you you are quite mistaken… (13)

I think it is too bad Emma ignored Mr. Knightley’s and his brother’s advice when it was given—now she has the mortification of realizing and accepting the numerous blunders she had made and in addition really embarrassed herself on Box Hill. I think Mr. Knightley did not give enough credit to Harriet for her good qualities at first (5) but he did revise his opinion at the ball:

"And, in return for your acknowledging so much, I will do you the justice to say, that you would have chosen for him better than he has chosen for himself. Harriet Smith has some first-rate qualities, which Mrs. Elton is totally without. An unpretending, single-minded, artless girl -- infinitely to be preferred by any man of sense and taste to such a woman as Mrs. Elton. I found Harriet more conversable than I expected." (38)

However IMO Mr. Knightley was not mean to say Harriet is illegitimate, ignorant and she is the child of nobody knows who because it is the truth. The poor consequences he predicted would come of Emma and Harriet’s friendship has also come true, especially the changes in Harriet:

Hartfield will only put her out of conceit with all the other places she belongs to. She will grow just refined enough to be uncomfortable with those among whom birth and circumstances have placed her home. I am much mistaken if Emma's doctrines give any strength of mind, or tend at all to make a girl adapt herself rationally to the varieties of her situation in life. They only give a little polish." (5)