How about instead of penalizing people who stay on the side with the largest numbers, we try using a 'carrot' approach and offer people perks if they switch.
Say its Sunday night and the the arena population is over 300, and the Rooks have 150 on. Can you imagine this MOTD popping up for everyone who logs in after the ENY limiter has kicked in:
Message of the Day
The Rooks' population is creating a numbers imbalance which adversely affects arena game play. Would you consider switching to Knights, for a one-time perk bonus payment of 30 perk points?
YES NO
If they answer yes, they are automatically switched to Knights and get the perk bonus. Granted, this idea would be more effective if the perk system was expanded and refined, so there was more incentive to gain and spend perk points.