It's an administrative punishment, so it may not be "extrajudicial" in the sense you mean. There might be no legal obligation to hold off until her appeal was ruled on. You can't delay getting thrown in the hole in a civilian prison by filing papers, so I really doubt you can do it in Fort Leavenworth.
I think the signal being sent was "We can punish your family and friends too. Imagine the anguish they'll feel not knowing where you are, or if you're even alive or dead."
Kind of like taking hostages.