I would suggest that if you're able to you rather change the Aboriginal peoples to be historically accurate than remove them outright. Indigenous groups have been documented warring against each other even before European contact (the Bunurong and Kurnai), and there is evidence of trade which stretched across the continent. Both sound like features a playable country would need in this game.
Australian Aboriginals are underrepresented in media, but projects like your game could help others understand their history and culture.