You can delete the home directory... it is the same concept as vfiler0 (physical controller) where both /etc and /home are written to the root volume. So, you could delete /home and recreate as a qtree. However, I wouldn't put any user data in the root volume... typically we create a very small volume for vfiler root then additional volumes for data... unless you are running cifs auditing or other vfiler specific logging (all controller logging goes to vfiler0 except for vfiler specific like auditing), I recommend you keep a small root volume and add additional flexvols with qtrees in them for the quotas.
I often delete the /home on root volumes (vfiler0 and vfilers) just to have only /etc in the volume so nothing else can fill up root...
