If you are on a *nix system then I suggest trying not worrying about it and see if it is all pushed to swap.

Two other possible solutions. The first is to tie some of your big hashes to DB_File. This is a minor code change but it will slow down access to the hash elements. However then they will be on disk, and not in RAM. The second is to investigate moving the part that needs access to the large hashes to an external script.