Wollstonecraft was largely respected for her early works, until word got out that she had been pregnant by a man out of wedlock. Then she lost much of her academic integrity, as people may had suspected her to be of ill repute from her views on the education of women, but that belief was confirmed by what would have been a scandal at the time. As such, it was much later before her views were taken seriously.

Also did Rousseau ever reply to Wollstonecraft?

Rousseau died in 1778, her book was only published in 1787.