Not sure why repatriation has to be so difficult, the problem is Morrison has left it to the free market and the free market has failed in a pandemic. So here's a suggestion:

First, determine where the Australians are. Give them a week to contact the local embassy. Not hard.
Two, Qantas and Virgin have plenty of planes sitting around that they would be happy to put to use. Have Australians pay a reasonable fare (payment deferred in cases of hardship) and govt can stump up the remainder so QF and VA can make a little money.
Three, those flights will arrive to an Australian city of the govt's choosing. Could be anywhere nationwide. Regional centres like Cairns have hotels and should be used. Quarantined for 14 days after which they are free to continue onward to their home state/city.
And ideally we need to curtail international airlines operating into Aus on the schedules they want. We have tried that and clearly it is too messy and potentially dangerous. Not to mention expensive for the Australians trying to get home.
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