You are obviously not used to dealing with thermal expansion in other designs, but this has been done time and again before so from an engineering point of view this is mostly a solved problem and not a 'big deal'.
For instance, you could have periodic sleeves that can slide over one another so you don't end up with the expansion on the final endpoints accumulated, the trajectory could be adjusted to allow for translation of some end-to-end expansion into a sideways expansion (much like what you see in long runs of heating tubing where they throw in the occasional U or loop to make sure the tubing stays put on the longer stretches) and so on.
There are a lot of really hard technical challenges involved in the hyper loop concept, I'm not sure why you'd focus on the thermal expansion as the major one, it's trivial in comparison to some of the others.
Btw, in railroads (that other long distance transportation method) the expansion is dealt with by putting a small gap between two adjacent rails. That's obviously not possible with the hyper loop as it is currently envisioned but I think that the answer is in there: don't allow the differences to accumulate over long stretches. We already have plenty of long pipelines, this one is just a big bigger in circumference.