Does the fact that we can only measure the two-way speed of light undermine the axiom of invariance?

There-and-back measurements still show the effect of an aether, because you can compare the results in different directions. For example, there-and-back along the direction of motion would show a different speed from there-and-back across it. This was the approach taken in the Michelson-Morley experiment.

The bottom line is that this is the wrong question to ask. You don't ever prove an axiom in physics.

You're not quite right about the ether: while the first order effect cancels out in "there and back again" experiments, the second order effect doesn't, which is why the Michelson-Morley experiment stood a chance of testing for the ether. But Michelson-Morley wasn't the end of ether theory, because you could always add fixes to account for the results. For example, the famous Lorentz contraction in special relativity was originally invented for ether theory; the idea was that flowing ether physically squeezed objects smaller. Einstein just took effects like these more seriously.

Ether theory limped on for another 40 years, getting progressively more complicated as more results came in. Ether was not abandoned because it was disproven by experiments or because special relativity was proven by experiments, because this never happens. It was abandoned by the 1930s it could only explain experiments using tons of epicycles, while special relativity just worked perfectly out of the box.

That the one-way speed of light is not observable plays a large role in keeping various relativistically-correct aether theories alive. Like general relativity, these new aether theories locally reduce to special relativity in the absence of nearby massive objects. Unlike general relativity, these new aether theories have a preferred universal frame of reference, typically a frame co-moving with the cosmic microwave background radiation.