After beating the game for the first time I unlocked every single achievement except pacifist! The only time I killed normal enemies was in the last boss, maybe I killed an enemy by accident. Anyway playing again on easy will be very very fast and this time I don't need to hide all the time, complete sidequests or collect ebooks!
EDIT: after some research for my new playthrough on easy I found that if enemies die on last boss fight it might prevent pacifist to unlock, so I reloaded a save before last boss, switched to easiest difficulty and beated it as fast as I could. ACHIEVEMENT UNLOCKED!
So if pacifist doesn't unlock for you try to beat last boss without any enemy dying to see if it unlock before attempting a new playthrough!
Thanks for the guide, it was very useful!