I agree the response by the Indonesians is a little harsh, but it's their country after all.
It seems no different to what Australia would do with illegal immigrants in similar circumstances - which may account for the sentences?
With the pilot's years of experience in PNG, the Torres Strait and other parts of the world, I can't believe he thought he'd get away with it? Seems a very stupid decision.
The Australian Government will offer Consular assistance but they can not intervene in another country's legal system.