You are right in that there is no way of specifying a 'Folder Name' as an exclusion basis.
However the user's Home Directories sync issues could potentially be caused by due to too many files that have been archived having to be synced to the users local machine (especially if it is a new machine / user profile, thus maxing out the maximum number of files recalls a user is allowed in a 10 second window. You can modify this by playing with the following registry keys on the file server where the placeholder service is running:
HKEY_LOCAL_MACHINE\Software\KVS\Enterprise Vault\FSA\PlaceholderService
RecallLimitMaxRecalls = 20
RecallLimitTimeInterval = 10
I would set the RecallLimitMaxRecalls to a much higher value for starters.
This way you should be able to allow users to download loads of files. Might put a bit of strain on your EV server but once they have fully synched that should stop.
Cheers