Sorry, I'm a bit confused because what you are asking seems contradictory. It doesn't sound like you want to
stop compilations -- instead, you want them!
If you let iTunes organize your music and you mark an album as a compilation, iTunes stores all the music in one folder based on the Album name, regardless of the artist. To make all the tracks of an album as a compilation, you need to select all the tracks (if may help to sort by album name), then right-click and select "Get Info". Make sure the pulldown for "part of a compilation" is "yes", and click OK.
If you have a compilation album with a bunch of different artists, but you do not mark it as a compilation, iTunes will store each song separately in each artist/album folder.
HTH,
Rob