"There is no fly."
It's hard to say. Placing "нет" second is more natural in such sentences. "Acceptable" is tricky to define.
«Есть муха — нет мухи» is a sentence twice as long as the one provided here ;).
That was meant simply to question you statement. "Мухи нет" is a meaningless statement without some context, people don't utter it out of the blue. I've provided a particular context.
Most word orders can have some justification. However, treating a sentence as if we meant it to be a part of a larger sentence is not a good way to determine the most natural word order, since a part of a sentence may have a different emphasis.
For example, «Есть муха» is also quite unnatural, and only in «Есть муха — нет мухи» they finally work together. Such an arbitrary choice of context will not work very well for a learner because a learner does not know which context would be OK for their word order. This is why we encourage to stick to a more neutral word order (which is a thing, and it is A1-level material, AFAIK).
It does not matter, of course, because we do not have this sentence in the course.