I have a client that requested we change the include path to a folder under his accounts directory. Adding this in the .ini file will make the change effective for all the accounts on the server. Is there a way to do this so that it is only effective for this one account?

You can modify the .htaccess or httpd.conf file.
See: http://www.php.net/manual/en/configuration.php

You can add the following in httpd.conf inside the <Virtual Host..> tags for client:

<IfModule mod_php4.c>
php_admin_value include_path "the_dir_requested:."
</IfModule>

Let me know if it works :)

UNTESTED :D