The real answer is to have desktop applications that work like applications (buttons do what feels right), and websites that work like websites.
SPA, is a page application. Pages aren’t applications, applications aren’t pages. AutoCAD is an app, the Robotech Encyclopedia is content.
If the browser only allows adding at most one history item per click, I should be able to go back to where I entered a given site with at most that many back button clicks.
At a first glance, this doesn't seem crazy hard to implement? I'm probably missing some edge cases, though.
That's not perfect, and it could still be abused, but it might prevent the most common abuses.
EDIT: apparently Chrome tried that and it wasn't sufficient: https://news.ycombinator.com/item?id=47761349