The Commander of any aircraft will know details of any special passengers onboard regardless of who they are at a briefing. PNRs (Passenger names lists) are made available to the crew prior to departure.
We believe that if they are made aware they may want a chance to consider the welfare and human rights issues involved in this case.
Sadly you are wrong. Welfare, legal and human rights issues are the resonsibility of the authorities, not the carrier. Their job is to take them from A to B safely.
Any views on how commonly this information is shared with Pilots by their airlines would be of great interest too.
Crews will be made aware of the situation and seating will have been assigned to the passengers concerned. Crews are not above the law and cannot intervene in such cases.