I do like SoCalPubbie's speculation, but on reflection, there's an obvious problem. If the aliens taught the ancients to levitate rocks to build large structures, they would risk the power of pi being turned on themselves, with large rocks and even astroids being hurled intergallactically to smash the home plant. This is presumably how the Bugs did it in Starship Troopers -- is there a more plausible explanation? -- and since the aliens had undoubtedly time-travelled, we must assume they'd seen the movie and would know better than to incur that risk. So as attractive as your theory is, I'm still open for additional explanations.
The ancients had their fair share of Einsteins. I don't know how the uber-brilliant think, but perhaps such questions just occur naturally to them as they sit around fires poking at the coals with a stick: "H'm. The ratio of the circumference of a circle to the diameter. That's an interesting question. I wonder if I could figure it out, and without algebra and decimal notation. That would be way cool." If you are smart enough, maybe you really think that way. But I'm still looking for a more mundane theory.
How old do you think the “science” behind a structure like Stonehenge is?
Examples of henges made of wood have been found not only in Europe but along the east coast of the United States. Is this knowledge of the Sun and Moon only 30,000 years at its oldest, or is it very ancient and even known by the Neanderthal people. The reason I bring it up is that henges are based on a circle, and knowing the degrees along the edge of a circle would be important to determing seasons, moon phases, and lunar/solar eclipses.
Ancient peoples may have had sophisticated mathematics because they were observant of how the natural world around them moved, and wasn’t static.