I don't think it's such a stretch to say that a digital copy is artificial, especially with the given context of malfunctions and personality alteration/memory deletion (and stuff I can't quite put into words, like her existing for so long and doing testing when no other scientists are left). Even Wheatley seems more human, though stupid and ultimately just as malicious.

I mean I could've seen the story written differently (and perhaps some of it was played for laughs) but that's not what it was.

@Chais