I have a domain.com/index.php and a friendly url rule to redirect domain.com/index.php?s=? requests. I use IIS webserver with the URL rewrite add-on.
Above works fin
Taking a look here you could add this rule so when a request that you don't want to process comes, you can ignore it and stop processing.
It should be placed first so that this rule executes before the other two.
<rule name="block" stopProcessing="true">
<match url="^admin/cloud/index.php$" />
<action type="None" />
</rule>