So after some serious thought about the conjoined twins dilemma, I think I have a solution. We punish the twin, seperate if its feasible, and if its not feasible, we still punish the twin, knowingly punishing the innocent twin as well.
Now that seems pretty hard-hearted, but here's my reasoning. Punishment is rarely ever without "splash damage", affecting those around the punished. Family, friends, co-workers, etc will be affected by this person's punishment to varying degrees. Family may feel as if they are being punished because of the person's removal from their lives. Sure we give them visitation rights, but its not quite the same as going out to a movie with them.
Similarly, if we must punish an innocent person (which we do in the normal course of punishment via family relations) to punish a guilty person, then it seems fairly consistent to punish the innocent twin along with the guilty twin. If we can seperate the twins, then we should do that, so that we reduce the punishment on the innocent twin. The surgical seperation amounts to the social seperation that the families experience. I'll admit that there is an additional layer of complexity between surgical seperation and social seperation. And to reduce the problem we can even make the surgical seperation optional. The innocent twin can choose to be surgically seperated or not.
In cases where seperation is not possible... Seperation might still be considered if the crime is a capital crime. The only reason why seperation is usually not possible is because it would result in the death of one or more of the twins. In the case of a capital offense, if the guilty twin can be surgicially removed from the innocent twin, resulting in his or her death, then essentially the death penalty has been carried out. If the innocent twin is the one that must be killed, or both twins would stand a good chance of dying in seperation, then a life in prison sentence seems more fair, again dependent upon the choice of the innocent twin (maybe s/he would prefer risking a deadly operation to life in prison).
Surely most of what I'm proposing isn't legal.... but I think it might be morally permissible.