It's Machiavellian, pure and simple. Everyone seems to overlook the line, "Therefore, you will not be destroyed." After the fight, the winner was to be destroyed by the Metrons.
(Let them fight it out so that we can learn who is most dangerous, then eliminate them.)
The Metrons could have wiped out both parties anyway. The "hypocrisy" of the Metrons was probably socio-political commentary. Remember that this is STAR TREK. How is this interference any different than the number of times Kirk violated the Prime Directive, all with the best of intentions because he knew what was right for another people?
Then there's my favorite line from "Conscience of the King" where Kirk asks Lenore, "Who do I have to be?" I'm not a moral relativist. I believe in leaving others alone, but I also believe in self-defense. Those offering rationalizations for their actions (like the Metrons) must feel their actions are questionable.