Controlling fruit fly in stone fruit in home orchards is always a challenge even when chemical control is resorted to. When the reason you bother growing your own fruit is to avoid chemicals in conventionally grown shop bought produce then chemicals are not an option. We must have tried every organic fruit fly control method but our tried and tested one is fruit fly netting. We purchased some netting from net pro in Stanthorpe QLD after learning of it from an organic gardening friend who had purchased lots of their offcuts to save money. It is not a cheap option however the net will last for many years and it really is the easiest and effective way to enjoy fly free fruit. It has the added bonus of keeping the birds off your fruit as well. It is easier to cover and uncover the trees if you make a couple of poly arches over the tree to support the net. We have planted our home orchard in a configuration which will eventually lend itself easily to netting the whole area rather than individual trees.
We love nourishing our fruit trees with the biodynamic tree paste we source from Biodynamic Agriculture Australia. For more information on this product check out their website. http://biodynamics.net.au/resources/biodynamic-paste/
Here is a photo of our trees covered in this wonderful paste after pruning.