She had held.
You are mentioning something which happened before something else (both in the past).
She vacated the role which she had held since her husband entered jail.
However perhaps you should add more detail.
"Anwar was formally charged earlier this month, just after his wife vacated her position/role in the Permatang Pauh constituency -- which she had held since he went to jail -- to allow him to return to parliament after a decade-long absence."
Without this additional information it isn't entirely clear what Anwer vacated.
I am not a teacher.
Student or Learner