I strongly object to them having mine - I am not a criminal (or at least I have not been caught yet) --
That train has already left the station. E.g. If you renew Driving License in most large cities RTO stores digital fingerprints+ photograph. If you register any property transaction in Mumbai, you have to supply digital fingerprints.
All this system does is, it centralizes this storage and reduces cost since each govt agency does not have to roll its own solution.