A full wipe is unavoidable as far as I can tell, as you either need to install LineageOS or try to do this via a rooted Graphene (both require a bootloader unlock).
In the linked Google issue tracker the links to the custom LineageOS builds are dead. I'm not sure how people managed to simply "install version D.2.0.23" of the eSIM updater app... it was a huge headache for me. I even tried (reluctantly) logging into Google Play to try and get an OTA update, which didn't seem to work. The latest version I could extract from official Pixel images was D.2.0.22.
I finally managed to fix my Pixel 9 eSIM - steps documented here. Hope it helps someone! (note it might, in theory, be possible to do all of this using Graphene alone. I pivoted to Lineage part way through, but I see no reason the final solution shouldn't work entirely on Graphene).
Note for devs: the underlying system package & user facing eSIM updater app both seem to not have the necessary network permissions to carry out updates. I did some logcat to inspect what was happening and saw failed network requests when trying to get the chip firmware updates. Perhaps giving these components network permission would allow whatever fixed the eSIM on the official Google OTA (mentioned in the linked issue tracker) to function?