As long as the biometric data is held only by a government agency, and not shared with the airline, I don't have any issue with this. If this is implemented correctly, the airline should only get a response saying who the passenger is, or an error if they aren't recognised or aren't on the manifest for this flight.

Passports already store biometric data, which I assume is also stored in some government database when you have it issued, so I don't see what's wrong with using that for something useful.