When She Woke is a re-imagining of Nathaniel Hawthorne's The Scarlet Letter, but it is also heavily influenced by Margaret Atwood's The Handmaid's Tale. In Jordan's dystopian future, a sterility epidemic has caused an under-population crisis. In some countries women are subjected to forced insemination. In the U.S., Roe v. Wade has been overturned, and the government has devolved into a dictatorial theocracy.
A feature of this new society is a process called "chroming" -- a form of punishment alternative to prison, in which citizens are punished for their crimes by being dyed a color relative to their offense. These "chromes" are then shunned, discriminated against, abused, and in some cases hunted once released back into society. Hannah Payne (think Hester Prynne) is guilty of murder in the eyes of the people: she had an illegal abortion to save the reputation of the already married father.
Not everything about chroming or the logistics of this dystopian world really sticks together or remains believable from beginning to end. But it's not meant to be. It's more of a plot-device to explore the concepts of guilt, faith, and dogma.
Some might consider the novel having an anti-Christian slant, and it definitely focuses on questioning the standard practices and doctrine of evangelical religion. However, I wouldn't consider it anti-god or anti-faith. The protagonist is a deeply religious young woman who, through her chroming experience, comes to question and ultimately rebel against the theocracy governing her. Her faith in god is explored, but never completely denounced.
Similarly the novel takes a pro-choice stance, but acknowledges the complexity of the issue. Hannah retains a feeling of personal guilt and responsibility for her action which she explores, while simultaneously refusing the guilt placed upon her by the puritanical society she lives in.
Jordan provides the best answer for the abortion argument: "It's personal."
...the procedure. Hannah remembered how the term, along with the other equally clinical and dispassionate words he'd used, had calmed her. She saw in retrospect that they had in fact enabled her to go through with it. You didn't temporize, much less agonize, over a procedure, you proceeded with it. A procedure didn't induce regret or require expiation. But how different the scenario became when you substituted words like "murder" and "abomination." The truth of it, Hannah thought now, lay somewhere in between. She'd ended her pregnancy out of love and fear and necessity. It hadn't been simply a procedure, but neither had it been an atrocity.
I would consider When She Woke to be YA fiction, despite it not being classified as such. I'm sure the publishers decided not to market it this way to avoid controversy with parents over it's subject matter. But everything about the way it's written and the way the subjects are approached point directly to YA. How disappointing that a book which could help young adults work through issues of faith and sexuality won't find it's way into their hands. I'm sure if the book was about actual murder, full-fledged and gruesome, it would be sitting right there on the school library shelf next to Twilight.