Obviously, if you can get to the outer reef and Coral Sea, it's a no-brainer. Do it.
However, I think that the day trip reef destinations are nowhere near as bad as people make them out to be. We went out with Deep Sea Divers Den out of Cairns in November and I was expecting a pile of dead coral and one very annoyed looking nemo. But that wasn't what we got. The reef was in really good condition and had plenty of life in and around it.
The company we went with is one of the smaller ones and do a one night (or more) liveaboard on the ribbon reef which gets you a night dive and couple more dives than doing two day trips. If you do go with them, the live-aboard boat requires a giant stride entry from about 5-6ft, which may be a factor for you.