I think Mr. Knightley sees Harriet’s position in society as a fact and in speaking of it to Emma is merely relating it as a fact not as disparagement of Harriet. He is not belittling Harriet rather his purpose is to give Emma a reality check:

"Whoever might be her parents," said Mr. Knightley, "whoever may have had the charge of her, it does not appear to have been any part of their plan to introduce her into what you would call good society. After receiving a very indifferent education she is left in Mrs. Goddard's hands to shift as she can; -- to move, in short, in Mrs. Goddard's line, to have Mrs. Goddard's acquaintance. Her friends evidently thought this good enough for her; and it was good enough. She desired nothing better herself. Till you chose to turn her into a friend, her mind had no distaste for her own set, nor any ambition beyond it. (8)

I do not see that Mr. Knightley gives the opinion Harriet has no chance to rise out of Highbury’s second set rather he quite accurately describes the situation in which “somebody” (3) has purposely placed Harriet. Harriet’s anonymous benefactor has educated and settled her as a parlor boarder with Mrs. Goddard to live in that lady’s set. There is no indication “somebody” destines Harriet for further greatness and this was all acceptable to Harriet and her friends until Emma came along. How is reminding Emma of what her friend’s real situation in life is as opposed to the fantasy Emma created disparaging Harriet?