The King Slayer (The Witch Hunter #2) by Virginia Boecker
This book is an excellent conclusion to the two book series. Elizabeth no longer has her stigma, and must learn to live without it's self-healing properties. John, who now has the stigma, is changing due to Blackwell's magic, and Elizabeth wishes to save him and kill Blackwell. There is war and romance, magic and transformation and growth of the main characters.