Two interpretations:
* "in"
her eyes are located in the middle of the extent of her light skin
* "plus"
she has light skin as well as kind looking eyes
If you take the second interpretation, the sentence becomes grammatically incohesive, but sounds not bad in literary writing.
In fact, I was able to find an example of similar "in her pale skin" in a novel called Kings, Queens, and All Their Things: A Drag Shergi Mystery, so I guess it's not immediately a weird English ... is it?
> She had scarlet hair cut around her face then the rest fell down her back. There were brown eyes **in her pale skin**.