I doubt the Netherlands had the amount of control over Indonesia as the French had over Indochina that they could just simply allow the Australians to take over. I doubt the populace would agree, and there was a lot of populace. The Australians would have to occupy, and they don't have the numbers for it. Nor do the British at that point.
The Australians also couldn't have done much better defending Indonesia than The Netherlands did against Japan. They would just be stretching their forces thin, endangering New Guinea.
Plus, it would mean the absence of the Dutch navy, although they didn't stand a chance it would make the job for the Japanese more easy.