It's the same deal - print the ID (the internal ID, not the Winbox # column!) of the script you'll be running, and pass it to the run command.
With the client from my signature (dirty installation: download it, extract the "src" folder somewhere, create the following file in the same folder), you can disable an account with:
<?php
namespace PEAR2\Net\RouterOS;//This must remain at the top of your PHP file!
require_once 'PEAR2/Net/RouterOS/Autoload.php';
$client = new Client('172.17.10.2', 'user', 'pass'));
//The key bit... getting the correct ID by printing it
$id = $client->sendSync(new Request('/ppp/secret/print .proplist=.id', null, Query::where('name', 'areeb111')))->getArgument('.id');
$disableRequest = new Request('/ppp/secret/disable');
$client->sendSync($disableRequest->setArgument('numbers', $id));
//And you're done.
(replacing the "areeb111" part with the actual username you want to disable)
To run a script, the code above will be the same, except that "/ppp/secret" will be replaced with "/system/script", and "/disable" will be "/run" instead.
Try it!