I've put the Zend library folder into classes folder of my app and renamed all files and folders to lowercase ( using Ant Renamer ).
When I call Zend_Feed, instead of loading /classes/zend/feed.php, kohana loads Zend from my servers share\ZendFramework\library\Zend\
(Zend Server), so I get a Cannot redeclare class Zend_Uri_Http
error.
ZF version; 1.10 Kohana version: the most recent files available through GitHub
Edit: Solved, look at my answer below. Just modify the original auto_load in order to do whatever you want to :)