Hopefully the headline is not as bad as the reality!
The penalty for breaching the Biosecurity Act is either a fine, or jail time, or both. It's not a special provision levied solely at returning from India. The penalties are designed for people who intentionally contravene the Act. It's not just travel, it's also our agriculture, animal and plant health, and environment that can carry penalties for people who deliberately contravene the rules.
The only way to get to Australia once flights are suspended will be via a transit city. For those unaware of the flight restrictions and somehow manage to board the fines probably won't apply. But for those deliberately contravening the restrictions, they may be subject to penalty.
The maximum penalties are there to cover a 'worst case scenario' - which could be a person gets a fake PCR result, gives misleading information to authorities and the airline in India (says they are only travelling to DOH, but in fact intends to go to Australia), and then infects people on the DOH-Au leg. Should that not carry some penalty?