Leaving aside the rather hysterical tone from the website, this looks like it has been a child's incident that has been allowed to get out of hand.
I know that the Koran is not allowed to touch the ground, or be damaged or defaced in any way, and to do so is a blasphemy to Islam.
But i seriously doubt that schoolkids fooling about would know that.
In that case, they should be punished for the offence of damaging a book deliberately, simply because that is not how books should be treated.
It can be explained to them the seriousness of their action as a religious issue, because respect for others' religions is part of living in a civilised society.
In my view, involving the police was a step too far by the school, taking unintentional consequences to an unacceptable level which is inappropriate for the age of the youngsters involved.
A lecture to the whole school about respect for the property of others is appropriate, and in an RE lesson for the year group involved, discussion of the sanctity of the Koran to Muslims would assist in education of people who live differently from the way the majority of the population do.