"..Her form, though not so correct as her sister's, **in** having the advantage of height, was more striking; "

Marianne cannot be having a *not so correct* form because she has **the advantage** of height.

This would show a negative result of something positive/advantageous.

If the result of her "not so correct form" was the result of height then the sentence would not use the word advantage at the same time.

IMO then the sentence would have read;

"Her form, though not so correct as her sister's, in having the disadvantage of height, was more striking;

I read it as;

Her form, though not so correct as her sister's, in having the advantage of height, was more striking;

Her form, though not so correct as her sister's,[whose form was correct] in [because of] having the advantage of height, was more striking;

I know I'm as clear as mud here. :-/