This isn't actually a problem! We build gas pipelines all the time which suffer exactly the same problem. (and no, you don't want gas pipelines to leak!) You can use expansion joints, or grooved couplings that enable movement, and there are other solutions as well. I think the problem that people have is that they assume you need some really intense vacuum for hyperloop to work. .05 bar (the pressure at 60,000 ft) is fine, and so is some leakage into the pipeline, which you just have to pump out.