Similarly I once had a stressful few hours in London when I attempted to check in for a BA flight to BOM without a visa for India. I had been travelling all year and somehow had the idea I could get the visa on arrival. Luckily for me BA did not cancel the entire rest of my itinerary as they would have been entitled to do, but deferred my flight for 24 hours and told me to hightail it to the Indian High Commission to get the visa.
I agree with the people who are saying that if the OP doesn't get an inquisitive check in agent it will at least be picked up at emigration control when they will look in the Australian passport for the visa and entry stamp to India, won't find it, and then the game will be up.
May be best to forget the direct flight idea and find a third country to transit, on separate tickets, where if they want to see both passports they are unlikely to know or care that there is no entitlement to hold the Indian passport together with another passport.
