[eluser]TheFuzzy0ne[/eluser]
You can add some logic to the end of your config.php to dynamically change the allowed characters.
Code:
if (preg_match('/^(\/some_controller)/', $_SERVER['REQUEST_URI']))
{
$config['permitted_uri_chars'] = '';
$config['enable_query_strings'] = TRUE;
}
There are some improvements you can make to integrate that into your setup a bit better, but that should give you an idea of where to start.