It also seems like it's not git that's emitting scary creaks and groans, but rather GitHub. As much as it would be a bummer to forgo some of GitHub's nice-to-have features, I expect we could survive without some of it.

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.

In a compressed format, later commits would be added as a delta of some kind, to avoid increasing the size by the whole tree size each time. To make shallow clones efficient you'd need to rewrite the compressed form such that earlier commits are instead deltas on later ones, or something equivalent.