Reditech,
Hackers normally take out several key files in order to disrupt the site, and in my experience, usually don't get into the database (unless particularly determined - touch wood, I've not had that happen yet.).
The main exploited hole they find is when your file permissions are set to 777 - which gives public write access.
Easiest way to fix it is to reupload any files you know have been changed - usually the fastest way a Joomla site comes down is if they change the root index.php file, rather than other files in the site - so it might not be the template that's been modified, just the index.php page. Trying
www.rle.org.au/index.php showed that page was missing, so that's a starting point.
Essential reading on Security:
forum.joomla.org/viewtopic.php?t=102558
Patrick