There is already the concern that there may not be a large enough player base to make a system like this work effectively. Limiting parties based on allegiance could ruin it completely in the case that there is a large build up of pvp minded people on one side compared to the other.
I was kinda hoping people wouldn't stick with the guild vs guild mindset (I was told the guild comp on heRO has cooled off a bit?) so that this system wouldn't only rely on guild competition and rather, would see mixed parties forming. Pipe dream I guess.
Don't know if it'd fix anything but perhaps rather than forming teams beforehand, people would need to enter the waiting rooms with no party. Players would be randomly distributed between two isolated waiting rooms. Both sides would be given say a minute to organise parties based off of the people who find themselves in these waiting rooms. The teams would then be required to fill a waiting room, which would check for correct party size and make sure everyone is present in the waiting room, before warping people to the arena.
Other than this it really is up to the players of heRO to be honest enough to play fairly.