I don't know where you are getting your facts when you say "to a lot of people, killing is the worst thing you can do to a person" especially if the alternative is eternal confinement with no ability to move or even think freely.

That said, I just stated that as a counter to your principles argument. That type of confinement is also not aligned with the principles you speak of, yet they are doing it despite all the risk it entails, and the monetary cost too.

It's just general hogwash of keeping a villain alive so he can escape at a later time. There's no real depth of thought behind this.