How can I stop Mail.app from automatically downloading full messages?
You may try a workaround: users with high email count can configure their Google Apps accounts not to sync more than 1000 emails per label (or folder).   

Each user will have to:  


Go to their Gmail interface  
Go to Settings (by clicking on the gear in the upper-right hand side of the page)  
Select the Forwarding and POP/IMAP tab  
Look for "Folder Size Limit "and check "Limit IMAP folders to contain no more than this many messages" and select 1000 (or another number that seems appropriate)