Apparently they already have a system in place like the one I mentioned in the OP:
The system will work much like our Warmode system in The War Within, where we balance as many copies of the zone as possible and eventually any overflow of one dominant faction will end up on a one sided zone by themselves.
Source: https://www.mmo-champion.com/content...ehavior-Change
So the faction imbalance is actually not a problem. At least, officially (I'm not sure if it actually works )