Can you point me to where you see the wording "Washington D.C. Rebel"?
The only thing I can find on those records are a stamp stating that the records are part of the "Rebel Archives", handled by the "Records Division" of the "War Department".
EDIT - Disregard this last comment. The link provided in your sources takes you to the wrong person documents on fold3 - you might want to update that.
So, first we need to determine what they meant by Rebel. Considering that the CSA was a rebellion, it was common for CSA sympathizers to be called "Rebels". The stamps on the documents are also marked as "Rebel Archives", but the full name was along the lines of "Records of Confederate Executive, Legislative and Judicial Offices".
Did you also notice that there are 57 pages on fold3 for "Miller, Anna T"? It would be interesting to have some document those...