You can write single page applications that are fully aria aware, and we do. In fact we're legally required to, and our pages are audited before they're ever released to the public including for assistive technologies. Screen readers support JavaScript, and have for at least the last ten years.
As to users choosing to run without JavaScript? We simply don't support it. We support IE8 and above. You cannot even get to our site using Windows XP due to errors in the TLS negotiation (to avoid SSL downgrade). If users choose to disable a core part of their browser that happens to be a core part of modern web standards, then they shouldn't be surprised when sites using that part no longer work.