Upon thinking further about this it seems to me the problem is caused by guix deploy attempting to restart services as well as it can during deployment. When this fails deployment fails.
guix system reconfigure on the other hand does not do this (afaik). As a result it can complete. Once reconfigure is completed a reboot switches to the new system version and is then thus able to restart the services. If all this is correct, then the long-discussed guix deploy feature of service restart policies would resolve this issue elegantly: When a similar herd upgrade in future looms, a switch away from "restart running services" to "no restart services" or "reboot after deployment" would avoid this currently hard-coded failure mode. Food for thought perhaps, if my understanding is anywhere close to right, that is. Alex