I was thinking the same YodTavYod.  A pardon means that you did the crime.  Flynn has to go back to court and sue all the culprits including Herr Mueller.  I could be mistaken, but I remember reading somewhere that Sullivan had placed a gag order on Flynn which prevented him from spilling the truth on the rest of the story which would obviously expose the DS operatives.  Flynn just knows too much. That may be why Sullivan was so desperate in not letting go of General Flynn.