Repatriation flights landing at DRW aren't commercially dependent on freight, they are government funded.
But diverting commercial flights to Avalon or other regional airports means freight (which is what is making the flight viable) is delivered to inconvenient locations without the infrastructure to quickly deliver to where needed - adding costs to freight business. Or planes have to land at MEL, offload freight whilst passengers and crews remain on board, then fly on to the regional airport (or vice versa) also adding costs.
If you land at MEL and then drive passengers to remote location, the transport risk is the same as transporting them to CBD - possibly higher as a longer drive.
Realistically moving to solely remote Quarantine locations will mean loss of seats on commercial flights, those commercial flights will become freight only into capital cities, leaving only repatriation/charter flights so over all intake falls and even fewer aussies get home.