But then I thought that it can be read two ways. "More highly valued" could mean that while Lady Elliot was valued or even highly valued by her husband, Anne would be more highly valued than that if Mr. Elliot makes her his wife. I think that if Lady Elliot had not been valued at all, the word 'more' would have been left out.

Lady Russell probably observed the courtship of Sir Walter and Elizabeth Stevenson, so she has a basis for comparison even in that sense.

It could also mean that Lady Russell is acknowledging that Sir Walter is not capable of valuing a person as highly as Mr. Elliot is--not that he didn't value Lady Elliot, but that he did so in his limited capacity to admire or value anything other than himself. Mr. Elliot seems capable of admiring persons other than himself.