Did "handsome" used to mean something pejorative or negative, like in the time of Queen Victoria?
Good call to notice the different nuance of her times. It wasn't pejorative, exactly, but at a lower level. "Mere" physical looks. "Handsome is founded upon the notion of proportion, symmetry, as the result of cultivation or work; a handsome figure is strictly one that has been developed by attention to physical laws into the right proportions. It is less spiritual than beautiful; a handsome face is not necessarily a beautiful face." [Century Dictionary, 1895]
The meaning of the word has not changed. She meant he looks good but not great. Handsome means the same. He could look beautiful too without being handsome. He might have had more of an effeminate grace than rugged good looks.
It means the same as now, very good looking. No point in pulling it to pieces, she wrote as she felt at the time.