[eluser]tonanbarbarian[/eluser]
why not put some code into the config.php file that detects if the site is front or back end and set the 'enable_query_strings' accordingly?
or if you are saying you are going to have to build 2 apps anyway , front and back seperated, why not just split the ci app into 2 folders, one for each, and have the front use enable_query_strings and the back not