Australia is notorious for its ability to remain clean of plants and animals not part of the local flora and fauna, at least until humans started using aircraft and motorized boats to spread invasive species. An advanced species should be able to recognize this quality in Australia.
What you do is relocate all of the sentients to Australia and start your sterilization on the rest of the world, including the sea's so no water wildlife can carry the disease. You map the way the water flows around Australia and how any medieval ships would float and sail when leaving the land. Put warning mechanics like bouys in the water to monitor potential threats and use scouting aircraft and motorized boats to patrol any land medieval ships might be able to reach. Any ships that do not turn back upon seeing your aircraft and ships with a potential "godly" display of sounds and lights, you blow them to pieces with incendiary munitions to make sure any disease is dealt with. Preferably this is done while leaving witnesses who can keep the fear of going beyond Australia's sea's alive. You could make this message even more clear by monitoring important ports for potential long-range sail missions and when you spot one you rain godly death on such expeditions as they are leaving port so the story of why you shouldnt go out to sea spreads like wildfire and you reduce the chance of spreading diseases.