Unless there is a way to equalize opportunity, don't have 1st, 2nd 3rd. etc, but have tiers. If you accomplish a certain amount of damage you qualify for tier1 rewards. Everyone can get two purples, fine, but make that hard to do and make the mission have a decent rate of failure. This would give incentive for organized play and yet prevent over farming because there is a decent chance it will completely fail and you waste your time, plus daily cool down.
Yes, that could work. And I dont think it would be too difficult for the developers to implement.