I think I understand what you're after. Assuming I'm correct, you've got the same setup we have, and the simple answer is "Yes, it works"
Let's try for some ASCII art of a directory tree:
|-->Head Office Users
| |->Jim Smith
| |->Jane Jones
|-->Sales Office Users
| |->Anne Blogs
| |->Tom Blogs
What I think you want is to have all of your users (head office, sales, remote etc) synced with Alfresco, and all the groups, but you want to avoid having accounts created for computers etc?
If so, set the sync to start at
ou=Accounts,dc=root (ldap.synchronization.userSearchBase and ldap.synchronization.groupSearchBase) and it should just work