I have the same problem and have been concerned about it for a while:
Just wondering if you found a solution. I use gmail and it downloads all archived emails over and over.
My solution was to disable the offline files and leave all files on the server. It means that it takes a bit to search for emails and it kind of makes the mail app less useful... But it also doesn't take up too much hard drive space.
The other option is that if you are using gmail, there is a google labs thing that lets you disable imap on certain folders. Then apple mail will see and download everything except for the archive folder, obviously minimizing the number of downloads.
But then you can t see unruly archived emails and is again not the best solution, but perhaps one of these things may help you .