Eu acho que a "punição" nunca foi oficial. Se você ler a frase novamente:
Scrimgeour was later punished for this oversight, because the fact that the Ministry had never punished Dolores for her many abuses of power seemed to Harry Potter to reveal both its complacency and its carelessness.
Isto é sobre Harry não ser capaz de suportar Scrimgeour, como ele gentilmente lembrou quando Scrimgeour entregou o testamento de Dumbledore:
"I… regret your attitude," he said, looking Harry full in the face once more. "You seem to think that the Ministry does not desire what you - what Dumbledore - desired. We ought to work together."
"I don't like your methods, Minister," said Harry. "Remember?"
For the second time, he raised his right fist and displayed to Scrimgeour the scar that still showed white on the back of it, spelling I must not tell lies. Scrimgeour's expression hardened. He turned away without another word and limped from the room. Mrs. Weasley hurried after him; Harry heard her stop at the back door. After a minute or so she called, "He's gone!"
Harry Potter and the Deathly Hallows, chapter 7, "The will of Albus Dumbledore"
A punição, então, não estaria trabalhando junto com Harry e, por extensão, com a Ordem; talvez a Ordem pudesse ter visto a infiltração do Ministério pelos Comensais da Morte (via Thicknesse) e ajudado Scrimgeour a derrotá-los.
Se Harry estivesse em boas relações com o Ministério, Scrimgeour poderia não ter morrido.