Shallow clones themselves aren’t the issue. It’s that updating shallow clones requires the server to spend a bunch of CPU time and GitHub simply isn’t willing to provide that for free.

The solution is simple: using a shallow clone means that the use case doesn’t care about the history at all, so download a tarball of the repo for the initial download and then later rsync the repo. Git can remain the source of truth for all history, but that history doesn’t have to be exposed.