Enable Query Strings in Code Igniter
There are several ways to handle this.
Most People, and Elliot Haughin's Twitter Lib, extend the CI_Input library with a MY_Input library that sets allow_query_strings to true
You will also need to add ? to the allowed characters in config/config.php and set $config['url_protocal'] to PATH_INFO
see here: Enable GET in CodeIgniter
Codeigniter Reactor lets you access $_GET directly or via $this->input->get(). You don't need to use MY_Input or even change your config.php. This method leaves the query string in the URL, however.
I used a hacked index.php to recognise users coming back from Twitter, check for valid and safe values, then re-direct it to to a CodeIgniter friendly URL.
It may not be to everyones taste but I preferred it over allowing query strings throughout the entire application instead of just one particular circumstance.