There's a couple of choices open to make this just go away:
1. Let the traveller keep the miles as recompense for getting up early to go the airport in the first place, sitting in cramped conditions for many hours, waiting in lines etc.
2. Sign up to the airlines corporate deals, where the sponsor "company" ie. the govt in this case, keeps the miles, so the issue never arises in the first place.
3. Negotiate a deal with the airline so that the seat is cheaper, and no miles accrue.
What about "Tier points" though? Taking BA as an example, they award airmiles for every mile travelled, redeemable for free travel/hotels/rental cars etc, but also "Tier points" for loyalty. As an example, a transatlantic crossing gets 60 points each way in cattle. At 600 points, the Silver tier is reached. This gives a mileage multiplier for airmiles, and (a big benefit) access to the BA club lounges. At 1500 points, the Gold level is reached, which gives a bigger multiplier, access to the First lounges, guaranteed reservation (ie someone else will get bumped to get you a seat if necessary), and almost guaranteed upgrades. The point is, it is a benefit accorded to the traveller by the airline, and has almost no "money in pocket" value if airmiles are withheld. However, it has immense benefit in terms of ease and comfort of travel.
The airlines have been round the buoy many, many times on this, and know what motivates a (frequent) traveller to choose certain airlines, and certain routes. They're adept at it, because it's their business. Suddenly, it seems that Joe Public is jealous of public servants being accorded the same benefits as corporate travellers.