seb128 asked me to file this bug...
He noticed that the Gnome3 new user dialog does not support the encrypt-home-directory feature that was present in previous versions of Gnome.
To solve this, the new user dialog would have a boolean checkbox (defaulted to un-checked), which asks if this new user's home directory should be created. Talk to mpt about the wordsmithing. If checked, then you need to add --encrypt-home to the 'adduser' invocation. Before running adduser, you'd also need to ensure that ecryptfs-utils is installed.
For real security, you would also need to run (as root) ecryptfs-setup-swap, which would encrypt the user's swap space. This is necessary, as any files/data that gets swapped out to disk could be written in the clear, thereby circumventing the user's requested encryption. Further note that if swap is encrypted, hibernation should be disabled (suspend continues to work just fine).