The delete operation is simply, the only that you need is add MutationDelete annotation.

/**
 * @ORM\Entity()
 * @ORM\Table()
 *
 * @GraphQL\ObjectType()
 * @GraphQL\QueryList()
 * @GraphQL\MutationAdd()
 * @GraphQL\MutationUpdate()
 * @GraphQL\MutationDelete()
 */
class User implements NodeInterface
{