Emma does in fact have the very same argument with Mrs Weston in Chapter 14:

"He ought to come," said Emma. "If he could stay only a couple of days, he ought to come; and one can hardly conceive a young man's not having it in his power to do as much as that. A young woman, if she fall into bad hands, may be teazed, and kept at a distance from those she wants to be with; but one cannot comprehend a young man's being under such restraint, as not be to able to spend a week with his father, if he likes it."

"One ought to be at Enscombe, and know the ways of the family, before one decides upon what he can do," replied Mrs. Weston. "One ought to use the same caution, perhaps, in judging of the conduct of any one individual of any one family; but Enscombe, I believe, certainly must not be judged by general rules: she is so very unreasonable; and every thing gives way to her."

"But she is so fond of the nephew: he is so very great a favourite. Now, according to my idea of Mrs. Churchill, it would be most natural, that while she makes no sacrifice for the comfort of the husband, to whom she owes every thing, while she exercises incessant caprice towards him, she should frequently be governed by the nephew, to whom she owes nothing at all."

"My dearest Emma, do not pretend, with your sweet temper, to understand a bad one, or to lay down rules for it: you must let it go its own way. I have no doubt of his having, at times, considerable influence; but it may be perfectly impossible for him to know beforehand when it will be."

Emma listened, and then coolly said, "I shall not be satisfied, unless he comes."

"He may have a great deal of influence on some points," continued Mrs. Weston, "and on others, very little: and among those, on which she is beyond his reach, it is but too likely, may be this very circumstance of his coming away from them to visit us."

As the passage you quote indicates that the opinion expressed here is Emma's real one, I can only imagine that she was arguing with Mr Knightley for the sake of it. Either that, or she was arguing on behalf of her dear friend Mrs Weston, which seems likely in a twisted sort of way! She is warmly defending Frank in Chapter 18 as she knows Mrs Weston would like him defended, at the expense of her own opinion, even overdoing it at times.