Devil's avocado: No one picked up on it because Woobie!Amy was already a thing in the fandom and contradictory hints were ignored.
Counter to devil's avocado: If Amy was evil from the beginning, never felt true guilt, why the F did she have all those prison tats done?
Walking to the hospital in the middle of the night is not a sign of evil.
In fact, why did she even maintain her 'no brains' rule for so long?
If she had no particular problem with manipulating people any way she wanted, why didn't she just go ahead and fix Mark? Why all the fucking drama?
Conclusion: She wasn't evil. She had a conscience. Wildbow's just decided to write it out for the sequel, and is now retconning matters so she never did have one.
Clarifying point: I have no trouble with characters
becoming the bad guy. Have not read Ward, but it's possible to go down that slippery slope and end up as an irredeemable human being.
What I object to is her doing it
suddenly, or worse, "She was evil all the time, and you didn't know it."
That's lazy writing. And going through seven years after the fact to literally
change the story to fit his meta-narrative is disrespectful to us, his readers.