Are you talking about the organization within iTunes, or the folder structure on the hard drive - in your home folder/Music/iTunes/iTunes Music ?
You can change the grouping within iTunes by clicking on the column headers - if you sort by artist, it will rip apart the album (in view only, not folder structure). If you click on the "Album" header several times, you can sort "Album by Artist", which will group all compilations together.
Not terribly intuitive, but I was glad to see it worked.