The joy flight company is based at YMEN, an airport not one of the pads on the Yarra.
EN has class C airspace and is perfect for training and therefore every flying school in the Melbourne basin sends students in and out of there for training. For helicopters this is generally not above 1500' and fixed wing either at or not below 1500'.
I think one option would be to vary the routes in and out. But a flight over the MCG is a fantastic view, although it is what takes the aircraft over East Melbourne where a lot of the complaints are coming from.