I know I would be irritated if they only credited the direct miles. It would definately change my flying habits and airline choices.
On the other hand I have been on positive side of this concept with a mileage based One World Award. I was flying on a mileage based award ticket, up to 50,000 miles. The only way to get from AKL-PPT on partners was to go AKL-LAX-LIM-SCL-PPT a distance of 17130 miles but it only counted as 2544 miles against my 50K. Unfortunately I couldn't get the dates I needed so I didn't make it to PPT.