I concur..... if you want to dive the GBR, it's best done from a live aboard. Cod Hole and the northern ribbon reefs are good, though not as spectacular as other tropical Pacific diving.
Mike Ball runs a nice operation, I've also been out on the Nimrod and there are a few other boats leaving from Townsville or Lizard Island. If you have 3-4 days available, jump on a liveaboard.
If you are planning on diving out of Cairns, just be aware that you may find many cattle divers. 30 people on one bommie. If you are going that far, it's definitely worth getting wet though.
Other options to consider, depending on where in Australia your wife will be working:
Prosperpine - Dive the Whitsundy Islands
Brisbane - Moreton Island and Moreton Bay (interesting tropical and sub tropical mix)
Sydney - Dive Shelly Beach in Manly to see Weedy Sea Dragons. Good beach dives and some decent boat dives outside the heads.
Perth - Rottnest Island and the HMS Swan
Exmouth - Ningaloo Reef. Some of the best diving I've ever done.
Lord Howe Island - Flights from Brisbane or Sydney. Amazing diving in a World Heritage site, great birding as well.
Pro Dive is the leading local dive shop and they can offer many packages through out Australia. I've also had very good luck booking through
www.diversionoz.com.
Enjoy the land Down Under!
-Rob