The article mentions that some requested pages are less likely to be legit traffic (old commits) and more likely to have bot activity. Perhaps they could increase difficulty on those pages for the proof of work. Keeping the "current" at a lower difficulty allows most normal users to use the pages as normal, while penalizing the bots.
One other way I have been thinking of is just delay the delivery of the pages, either limit bandwidth or just wait for a bit until you deliver the page. For one user a (lets say max)3s delay on some pages is not a huge deal, however at scale that adds up and means the client can't gather other pages in the meantime.
Another option is to lock the out of date html renderings behind a login page while keeping the git openly available.