Wait witch is not that high of a problem to deal with if you don't want to align your self with lawful evil or chaotic evil. If you choose mountain lair you can get warlock and with him you have many ways to deal with the witch. No need to have high mercy or cruelty. My favorite way is to send possessed drunkard to overpower her. Not sure if you can just dump her in to prison after warlock has helped you to overpower her or is giving warlock her powers a must. Still witch is not a problem if you are worrying about being too lawful or chaotic. Not sure if infernal or eldritch ally's have ways to deal with her. Never tried because allying with them seems like obviously bad idea. I'm sure you bring some other similar example but this is a visual novel type of game absolute freedom is almost impossible to pull of in this type of game or if you want to have story of any kind.