Setting up drush ini path in my site alias
Drush processes drush.ini in the drush bash script prior to calling drush.php.  Here is the relevant code it uses:

for conf_dir in $(dirname "$SELF_PATH") /etc/drush $HOME/.drush ; do
  if [ -f $conf_dir/php.ini ] ; then
    drush_php_ini=$conf_dir/php.ini
  fi
  if [ -f $conf_dir/drush.ini ] ; then
    drush_php_override=$conf_dir/drush.ini
  fi
done


You will need to make sure that your drush.ini file is in one of those location in order for it to be found and processed.  Note that the drush bash script never acts on command line parameters; those are parsed in php.  There are some environment variables that affect the drush bash script, but there are no environment variables that affect the selection of drush.ini, and there is no facility in site aliases to pass environment variable values to drush on the remote machine.

Sorry.

Edit: You could try setting %drush-script in your alias file to point to a script on the remote machine that called php /path/to/drush/drush.php.  Read the advice in the README.txt for Drush-4 on how to make an alias to drush.php if you do this; you will want to make sure that --php is passed to Drush correctly, etc.