I have done this successfully using a custom php.ini with the non-shell method outlined here http://wiki.dreamhost.com/Custom_PHP.ini.
I created a cgi-bin and ioncube directory.
Erm, stick the ioncube loaders stuff in the ioncube folder...
Then use the non-shell method...
I then added the ioncube section as the 'first line' to the php.ini created by the non-shell method in the cgibin directory,
zend_extension="/home/user/ioncube/ioncube_loader_lin_5.2.so" (or whatever version)
/_/_ / (
( /( /)(/__)())(