In most instances, spotting a fly on your food doesn't mean you need to throw it out. While there is little doubt that flies can carry bacteria, viruses and parasites from waste to our food, a single touchdown is unlikely to trigger a chain reaction leading to illness for the average healthy person.
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If flies are allowed to lay eggs in food at any stage of food preparation, that would be a failure of process and would need to be addressed. “Fly eggs/maggots do not survive cooking processes and flies do not lay eggs/maggots on hot food, they do however lay on warm food.
Is it safe to eat food a fly was on for an hour if you microwave it a long time? Yes. As long as you don't mind the chance that you're going to ingest a very small portion of fly vomit and poop, then there's no problem.
At 120° or higher