The restriction comes from Google, and you know this.
The alternative with a fix in software would be to lose Google certification for Fairphone OS, which means not having Google’s Apps and services in Fairphone OS by default anymore as well as losing Google’s business obligation to react to any issues on their side.
That’s not a viable alternative for an official stock vendor Android OS.
Google uncertified Custom ROMs sporting full fingerprint reader functionality are available for users to switch to in case they want to prioritise the fingerprint reader over having the vendor stock OS.