BP:
I agree that HIS is not faultless. If HIS had thought this thing through, then they could have easily come up with a better solution (several of which have been proposed on this thread). But ANA and the ministry seem to be saying "nothing to do with us", which I think is crap.
HIS has basically come up with another version of the soapland argument mentality here ala "No Gaijin can come(

)in here because all Gaijin have big Penis'"
Depending on your situation, this is either a offensive moral issue, or sound economic policy.
The only real answer is as snobee says, and do away with this type of ticket. Seems logical, but you know as well as I do, what may seem logical to many of us doesn't sit well with these 50-something mid level managers.
Everyone here pretty much agrees that the idea of getting penalized for not using a seat that you have already paid for is senseless. But it is one of the conditions on the fare. Just because it is stupid doesn't make it any less valid when it comes to the contract you enter into when you purchase the ticket. All HIS had to do was make this clear to the buyer when they purchased the ticket.