In most Munchausens by proxy cases by and large, when the parent is closely watched, the parent is found to be deliberately poisoning or doing things physically that cause the child to be sick. A mitochondrial disease can be shown via lab tests. If the child is shown to be physically worsening under the state’s care, it may be that the state is actually in error.
As I understand it, Justina has never been confirmed through testing to have a mitochondrial disorder. From everything I have read, there are no real definitive tests for mitochondrial disorders.
One of the things that I have read about Munchausen’s is that the affected parent often homes in on a disease whose symptoms are vague, and which cannot be definitively ruled in or out by testing.
The bottom line is that we do not know enough about this case (having only heard one side of the story) to know whether Justina is genuinely ill, or if she has been made ill through the actions of her mother.