The upside for the airline is not the fewer miles awarded, rather the marketing effects:

- A flight that appears to be non-stop to a naive customer;
- A flight that gets display priority in GDS systems since it is "direct";
- A flight that results in additional booking because of these deceptive practices.

It's sad that the airlines have no intent of offering the flights as true "direct" service, and in many cases, even have a change of equipment at the stopping point, so there is no way it would have been the same aircraft anyway.

The only way they're going to stop doing this is if the government bans the practice, or regulates it thoroughly.