This can be vefified by looking at Trunk:
'users' => $wpdb->get_var( "SELECT COUNT(*) FROM wp_users INNER JOIN wp_usermeta ON (wp_users.ID = wp_usermeta.user_id) WHERE 1 = 1 AND ( wp_usermeta.meta_key = 'wp_{$blog_id}_capabilities' ) " )
you should be able to change this to:
'users' => $wpdb->get_var( "SELECT COUNT(*) FROM $wpdb->prefix_users INNER JOIN $wpdb->prefix_usermeta ON ($wpdb->prefix_users.ID = $wpdb->prefix_usermeta.user_id) WHERE 1 = 1 AND ( $wpdb->prefix_usermeta.meta_key = ' $wpdb->prefix_{$blog_id}_capabilities' ) " ),
This is untested so you may need to escape the $wpdb->prefix not sure.