Delete a WordPress network's site content when a single site is deleted.

delete-multisite-content.php

<?php
/**
 * Helper function to remove a directory and all its contents.
 * PHP requires you to remove each file individually and delete
 * a directory only when it's empty.
 * 
 * @param string $path Absolute path to a directory.
 */
function remove_directory( $path ) {
	$files = glob( $path . '/*' );

	foreach ( $files as $file ) {
		is_dir( $file ) ? removeDirectory( $file ) : unlink( $file );
	}

	rmdir( $path );
}

/**
 * Cleanup orphaned tables during site deletion
 *
 * @param $site WP_Site class for the site that was just deleted.
 */
function delete_site_contents( $site ) {
	global $wpdb;

	// Get the list of tables using the site's prefix.
	$table_list = $wpdb->get_col(
		$wpdb->prepare( 
			"SHOW TABLES LIKE %s;", 
			$wpdb->esc_like( "{$wpdb->base_prefix}{$site->site_id}_" ) . '%' )
	);

	// Loop through those tables and delete them 1 by 1.
	foreach ( $table_list as $table ) {
		$wpdb->query( $wpdb->prepare( "DROP TABLE %s", $table ) );
	}

	// Delete the site's uploads as well. 
	$upload_dir       = wp_get_upload_dir();
	$site_upload_path = $upload_dir['path'] . '/site/' . $site->site_id;

	remove_directory( $site_upload_path );
}

add_action( 'wp_delete_site', 'delete_site_contents' );