This is not some peculiar act of cruelty. When a horse falls all the way down, its immediate instinct is to get back to its feet as quickly as possible. This can be a problem if, for example, the horse is tangled in harness, or part of it is under a jump or other obstacle.
Gently pinning the head is the easiest and safest (for both the horse and the person doing it) way to prevent a horse from rising if you need it to stay down. With a big draft horse, this can take all or most of the person's body weight, hence "sitting on the head."
As horrific as it sounds, pinning the head can save a horse's life.