I'm working on a couple of sites with shops at the moment and have come across the same issue. My approach at this stage will be to create a Aussie translation file that replaces VAT with GST. Will submit back to eZ for consideration for inclusion into the core.
I've created a translation file for 3.8.7 and uploaded as a contribution. See: http://ez.no/community/contribs/internationalization/australian_translation_for_3_8_7
Will attempt to compile one for 3.9.1 over the next couple of days.
It does seem like overkill to create and utilise a translation to do this. Brendan Pike has an interesting solution of adding this term to the locale: http://issues.ez.no/8843.