Here is a win-win situation based on the Canadian principle of maximum satisfaction.
Since law does not forbid anybody from refusing to show face to vote at polls, Elections Canada could use either face recognition (present method), fingerprints, hand geometry or iris recognition. Veiled women and Halloween-masked men could refuse to show their faces at the polls, provided that they submit other human biometric characteristics. Thus, the method of identification would not be restricted to visual face identification by election officials, and religious freedom would be maintained without compromising the legitimacy of the electoral system. In effect, Muslim women wearing face-covering niqabs or burqas would be pioneering the biometric identification which will eventually be implemented in passports and such.