If you want to keep prisoners safely forever, note that you can add and then remove prosthetic limbs, which will keep them permanently immobile.

For clarity you only need to install and remove peg legs to achieve this effect.

Removal of tongues and the addition of Painscrews is optional.

I use this so taking the tongue is counterproductive. And the pain-screw is a waste of resources and medicine, unless you are making a scream nugget.