Conflict with site_url() in Codeigniter vs Wordpress

I've an app tightly integrated with Wordpress, - using the Wordpress authentication solution.

After upgrading from 3.1.6 -> 3.1.9 I got conflict with site_url() in Codeigniter

PHP Fatal error: Cannot redeclare site_url() (previously declared in /home/abfotqpq/public_html/konkurranser/system/helpers/url_helper.php:64) in /home/abfotqpq/public_html/wp-includes/link-template.php on line 2990

I commented out the function in url_helper which helped me. Any better solution ?

Rgds

Geir