The first thoughts of the Hogwarts administration must be, and are always, for the safety of her students. For hundreds of years, Hogwarts has stood not only as the pinnacle of education in the wizarding world, but also as a bastion of hope and a representative of what can be when all magical students, from all families and walks of life, are treated and educated equally.
In order to remain as she has always been, certain steps must now be taken to protect that way of life which Hogwarts represents. The long time refusal of the Ministry of Magic to accept the fact of Voldemort's return was the beginning of a dramatic sequence of events which have brought the Ministry of Magic to this repugnant, reprehensible point. The recent unchecked attack on the Ministry itself, the uninvestigated murders of Ministry employees, the propagation of unfair decrees against Muggleborns, and the recent release and acquittal of Death Eaters can no longer be borne in her overseers if Hogwarts is to remain acting in the best interest of the students herein.
For that reason, Hogwarts now rejects the control and oversight of the Ministry of Magic until such a time when the Ministry of Magic again represents what is noble and just in the wizarding world.