I agree with Sir-Prize that it might not be best to separate the ladder, if there are so few player to begin with.
My idea for a solution would be to make it opt-in. E.g. in the matchmaking tab there is Box A you can check, where you would like a 10% probability (or whatever) to play on a mapgen map. Box B would be if you want to always have a mapgen map and none of the ladder pool maps. So two players that select B can always play mapgen on ladder if they are paired, and any player that never wants it will never get it.
Just a suggestion, no idea how difficult this would be to implement.