I just had a sudden brain wave and realised that King of thorns is pretty much what your looking for. Its got transformations and characters going over to the evil/monster side
Spoiler (mouse over to view) About a girl thrown into a dystopian future where a virus has either transformed or wiped out all of mankind as far as the survivors of a cryogenic sleep can tell but the threat of the virus they went into cold sleep for is still imminent and to make it worse strange monsters are now roaming around the place. The virus changes type and becomes more of a transformation type as the story progresses and the main character has to come to terms with the monsters, transformed people and confront all the mysteries. The ending isnt siding with the monsters so to speak but she comes to accept them and does join up with a certain group of smarter ones
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