That's a fair point. I'm afraid I don't have a good solution. The obvious one would be Square punishing behavior like that so that people tempted to do it wouldn't do it for fear they get banned, but Square does so little moderation of their game I think that's unrealistic. I don't think any system can be made villain proof.
The commendation discussion and the higher rolls on loot discussion are two different proposed ideas in the thread, but don't actually incorporate each other. I suggested commendations being worth more (for example, cooler achievement rewards for them, using them as a currency for mounts and gear, etc) as a way to encourage people to perform better in duties instead of the OP's suggestion of a performance based roll bonus.