I have mixed feelings on the pronoun use, but having read some of her autobiographical writing I don’t think she would have taken much issue with it. This piece is more focused on her work in computer engineering, so I felt it was appropriate to post here.
One analogy to consider is when someone comes out of the closet as non-hetero.
Say you know a man called Joe Schmoe who used to live “in the closet” but eventually came out and said he was gay, he’d always been gay, and he’s ready to publicly proclaim his sexuality. You wouldn’t then look at a photo of Joe taken back before he came out and say “this is a picture of heterosexual Joe Schmoe” because he wasn’t heterosexual, he was a gay man who wasn’t yet able to outwardly live that particular truth. Past Joe was still gay, not straight, and it remains correct to refer to him as gay no matter when in his life you’re talking about. The error of his previous misidentification has been corrected, and his labels thoroughly (and retroactively) updated to reflect that.
Similarly, it’s correct to always refer to a trans person as their true gender, preferred pronouns, and preferred name, even if you’re referring to a time in their life when they were not yet living that truth. Lynn Conway was correctly identified as a woman with she/her pronouns, and this article does her a disservice through its mixed-up pronoun use.