How about make it no scoring until the arena reaches a certain number of players (say 50). Or make score a function (percentage of total players online). For example if Arena A has 150 players, and Arena B has 50 players, then you score 75% in Arena B, and 25% in Arena A. So the milkrunners would have to do 4x as much work. As the numbers balanced the score ratio would be 50%/50% in each arena.
It'd be very hard for HTC to have arena's opening and closing.