The hat was only used on the first years, we'll all be 6th years up so should be well sorted at that point but I do understand what you mean. There could end up being an influx of Slytherin and Gryffindor characters leaving Ravenclaw and Hufflepuff pretty much empty.
Perhaps a quota to start off with. Depending on how many members are interested and how many characters are allowed per member.
Maybe a start off point of 6 members per house - there are of course the npc students that get used to fill the place lol
If say Gryffindor has it's 6 member quota then a note can be posted stating that no more Gryffindors are being taken until other house quotas are filled or anyone else applying for that house will have to be notified that he or she must choose another house affiliation.
When all house quotas are filled, a new quota can then be opened.
It's just an idea