Great Question.

I've thought about this in the past, and it seems airlines actually consider mileage runners to be a beneficial force that can be used for a purpose....

1) There may be some routes that need to have just a bit more paid passengers during certain periods of time, to cost justify and keep open the route until competition or seasonality issues change

2) Passenger-seat miles and other reported statistics to the Financial Community can be "beefed up" for certain desired time frames for specific routings

3) Upgrades to Buisness Class probably cost VERY little vs the good will that it generates... particularly when the planes allotted may be 98% full some days of the week, but only 60% full others. Consider that on Transoceanic flights (today) they just can't downsize to a 737 from a 747/777! The number of business/first seats is pretty much set... and they are either empty or used... ( and the airline controls the award inventory )

4) It still can be profitable. If you owned a business would you like to make a sell at Cost+$50 or no sale at all? Most mileage runners wouldn't be buying the product at all if it weren't for the mileage run. As long as the airline can properly control the cost/rewards such that they make a profit over the long haul... it's goodness?

For example.. during TRIPLE MILEAGE Madness at United last year, a lot of folk mileage runned to Australia... and UAL seemed to be encouraging this. Stats went up on this route as a result....at a time when there was a lot of pot-stirring related to Australia access and service expansions.

Just some thoughts