Just create faction specific population caps in addition to the overall server population cap.
For example, if the server supports 5000 concurrent players, you can set it up such that each faction has a separate population cap (and corresponding queue) of 2500.
Suddenly the horde are in a much longer queue (if there is a queue).
You could even make the faction caps larger than half of the total server cap, which allows SOME imbalance, but not unlimited imbalance.
Of course all of this could only work if it were done basically right now. Wait a few weeks, and the larger servers won’t even have significant queues.