Bright Chen's Blog

This isn't really a real answer... I mean it'll get the job done... but there you have it.
gksu gedit /usr/bin/compiz

right at the very bottom it says:
${COMPIZ_BIN_PATH}${COMPIZ_NAME} $COMPIZ_OPTIONS "$@" $COMPIZ_PLUGINS || exec $FALLBACKWM $FALLBACKWM_OPTIONS

Try:
${COMPIZ_BIN_PATH}${COMPIZ_NAME} $COMPIZ_OPTIONS --indirect-rendering "$@" $COMPIZ_PLUGINS || exec $FALLBACKWM $FALLBACKWM_OPTIONS

In place of it.
This changes what it run at the end so even if the script sees that you should run with direct rendering, the final exec line has it within. Easier than hacking up the actual script.