The Emancipation Proclamation freed only the slaves in the Confederate states. Since they were no longer part of the Union at that time, then that order had no legal status.
If I divorce my wife, I am not responsible for any debt she would incur after that divorce.
What specific action would you like POTUS to take that he has not already taken?
Isn't it obvious? I would order DoJ to take Terri into protective custody and save her life. I know it would cause a constitutional crisis (though I highly doubt a "civil war" as you suggest), but it is time for that. The judiciary controls entirely too much power. It is time to put then back into their original place.