Star Cursed (The Cahill Witch Chronicles #2) by Jessica Spotswood (Putnam Juvenile hardcover, 18 June 2013).
Star Cursed continues almost immediately after the ending of Born Wicked, so if your memory is as bad as mine, you may want to reread the first book before beginning the second.
Cate Cahill has given in to pressure from the Sisterhood, and has joined them at their headquarters in New London. She's not at all happy about this, and feels lonely and provincial. The only student who is sympathetic towards her is her roommate, Rilla. She's mocked and bullied by Alice, the "leader" of the students.
Everyone except Sister Cora, the head of the order, seems impatient for Cate's powers as the prophesied Chosen One to manifest. Cate is pretty sure that it's not going to happen, but she much rather it be her than one of her younger sisters.
Meanwhile, Cate does the expected duties of the Sisterhood: visiting and providing comfort to the ill, indigent, and imprisoned. The power of the Brotherhood is growing; even the suspicion of being a witch is grounds for punishment, and people are disappearing more and more frequency. This book is much more political than the first, and descriptions of the agonies inflicted, especially against women, by the Brothers are more graphic.
Spotswood has taken the Seventeenth Century persecution of witches to an extreme in this gripping, read-in-one-sitting novel, but even more chilling are the parallels that can be drawn to today's attempts to wrest power from women.
FTC Full Disclosure: Many thanks to the Publisher for the e-galley of the book.