In my codeigniter config I have $config[\'global_xss_filtering\'] = TRUE;. In my admin section I have a ckeditor which generates the frontend content.
$config[\'global_xss_filtering\'] = TRUE;
E
Simple do the following on the views when displaying embedded object code like from YouTube and etc:
echo str_replace(array('<', '>'), array('<', '>'), $embed_filed);