Meaning: If beauty is her Yin, then intelligence is her Yang

Solution 1:

Yin and Yang are opposing forces, yes, but their relationship is not like "up and down", in which one is positive and another is negative: they're simply two forces meant to balance each other without any connotation. Yin and Yang are more "food and beverage" (complementary to each other) and less "good and bad" (mutually exclusive).

So yes, you can use those to describe positive traits

Solution 2:

Yin and Yang are not actually forces. In fact, they're not actually anything in and of themselves. the best explanation I can give is that they are the names given to the archetypal concept of opposites. Whatever is going to be called or considered Yang, its opposite must be Yin.

While it's true that certain classes of opposites have been traditionally assigned to one or the other of the 2 names by convention (such as Light, Day, Male, Active being considered Yang — and Dark, Night, Female, Passive or Resting considered Yin), this is always relative.

The English equivalent of Yang and Yin is Systole / Diastole (words which I believe were actually coined by Goethe), and which have been assigned by convention to the physiologic activity of the heart.

My sense about this sentence is that calling Beauty the Yin of Intelligence is actually saying that only ugly women are intelligent, and so in answer to the question

...Yin is typically negative and Yang is positive.... Is that right?

emphatically, yes, it is (by convention, only). also:

Can I still use it to describe two opposing but positive traits?

Yes, of course. That's poetic license.