As one of very few women in the field, and one of even fewer who writes primarily about women, I tend to think a lot of this attitude is a reflection of the extent to which sci-fi has been an "old boys club" for most of Atwood's career, more than it is about the genre itself
All of literature can be regarded as an "old boys club" if you squint, but it's not like she'd have been unique. "The Left Hand of Darkness" was published before I was born, but I was old enough to read "The Handmaid's Tale" by the time that was published, albeit not quite old enough to properly understand it.
In fact I don't think "The Handmaid's Tale" really makes sense without the context of the AP feminists. Gilead comes about, as I understand it, because the AP feminists think they can use the Religious Right to achieve their goals and unsurprisingly that goes badly for them. AP feminism doesn't even exist when "Left Hand" was published.
I saw her talk once and I thought this statement was more about her being glib. If I recall what she said correctly, it was “I don’t consider what I write to be science fiction, because something like it has already happened.”
But maybe that’s just post-hoc rationalization for a reactionary stance, idk.
One of the greatest sci-fi writers of all time is a woman. Most consider her to be the best. Ursula LeGuin.
And she absolutely is not the only one. There are plenty of very talented and very popular women authors in the genre.
Margaret Atwood just wants to be thought of as literary.
The handmaid's tale is without a doubt speculative fiction (SF), the umbrella term for writing that includes sci-fi, fantasy, alternative history, etc.