As Turbine, developer of LOTRO, released Mines of Moria the instances had a similar problem. They made some pretty nice dungeons wih good mechanics but parts of the community decided to EXPLOIT their way through the bosses.
The solution was pretty simple. A door was built in front of many bosses and a trigger group of enemies was placed/moved to the door. Those who ran had an overwhelming situation.
Giving more tokens for clearing all enemies is just not the solution. As long as the dungeon could be run in time X and be more efficient than killing all creepers...
SE put a good amount of time and work in those dungeons, let's praise em for that work.
If you're put in group with runners let em run, report em while they run. They mostly can't kill the boss without you.
Seriously: It is an EXPLOIT!