Didn't read thread, sorry.
Seeing a Muslim woman is ok if it's done by another woman. When ID is taken, a headscarf that allows the full face to be seen could be allowed, the staff in the room taking the picture should be women, and the image processed by women. Most countries have infrastructure large enough to be able to handle that requirement.
When people need to show ID, then female staff should handle it. If there are no female staff at a private business like a nightclub or bottle-shop, then too bad for the Muslim woman. That shouldn't be too hard on Burqa wearing women anyway.
At official sites, there should be plenty of female staff around to handle peeking under a burqa. Airports, government buildings, etc.
If a policeman sees a burqa clad individual behaving suspiciously, on the street or elsewhere, he should be able to detain the person on the spot to wait with him until a female officer can turn up to speak face to face with the person.
Burqa wearing drivers might have a harder time of things, having to wait around more, or to go into police stations more often to be processed, rather being processed on the spot, but c'est la vie.
Anyway, what I'm saying is that compromises can be made so that only other women see under burqas. As for Headscarf wearing Muslims, their ID should be taken with the Headscarf on. The only reason non-Muslims are asked to have their heads bare and not to smile is so that the photo will match with your face in your most usual state when you are walking around. (as well as so that the face isn't partially obscured in the ID photo). Since Muslim women will habitually and usually be wearing their scarf, then it makes sense that their ID photo displays them wearing one. Also, most Mulim scarfs are sleekly pulled away from the face, leaving it unobscured, so that there should be no face obscuring problems.
