No, this is poor thinking. While you might say it made some sense to use a supernatural story to explain why the universe is as it is, it was not 'perfect'.
No theory about the nature of the world is perfect, PC. Even science, by its nature, is an
incomplete, and therefore 'imperfect' explanation of the world.
The arguments about why a universe exists if it implies something coming from nothing also apply to the supernatural beings.
But the supernatural beings are, well, supernatural. Their Being is therefore not the same as the Being of the observable world, and does not require ontological grounding.
It's simply wrong to say a coherent atheism "couldn't be thought". "The universe just is" is just as coherent as "there was a prime mover". Strands of Buddhism managed without supernatural beings ordering the universe.
Buddha got around this problem by proclaiming the mysterious Being of the world to be an
illusion, Maya. The essence of all things, the essence of our own experiences and our own being, is sunnyata, emptiness. It therefore requires no ontological grounding. Yet even Buddhism degenerated into a folk religion with gods and demons and all sorts of supernatural entities. And most Buddhists still regard the Buddha as being 'up there', somewhere, watching over his faithful followers.
The scientific method makes it easier to see that supernatural explanations are unnecessary. I don't think it's any form of philosophy that has encouraged atheism, so much as psychology that shows us how people frequently fool themselves, and sociology that describes how societies use ideas to tie themselves together, whether or not they are logical. It's easier to step back and examine unspoken assumptions about the truth of the religion you're indoctrinated into.
While I think there's some truth to that, it was the transcendental philosophy of Kant, in particular, which made atheism intellectually respectable (though Kant himself was not an atheist). Kant demonstrated that the form, the shape, of what we experience is actually a projection of our own minds onto the chaotic jumble of sense-impressions which we experience from moment to moment. Even such fundamental things as 'space' and 'time' are merely "forms of thought" which we project onto the phenomenal world to make sense of what we experience. Schopenhauer called this Kant's "Copernican revolution" - from thenceforth, there could be no rigid distinction between the world "out there" and the nature of our own subjectivity. The noumenal world is unknowable and can be bracketed as metaphysics and therefore requires no ontological grounding, and the phenomenal world is a projection of our innate "forms of thought" and therefore
also requires no ontological grounding. Who needs God?
@noemon : Epicurus did not deny the existence of the Gods. He merely said that they are distant and are unconcerned about us, so we should likewise be unconcerned about them. This is, I suppose,
practical atheism, but is certainly not
theoretical atheism.
"Politics is the art of looking for trouble, finding it everywhere, diagnosing it incorrectly and applying the wrong remedies." - Marx (Groucho)