In the samba config you can specify where you want the mount points to be - there is no obligation to support user home directories if they are not needed. There is usually a rule in the samba config file you simply need to remove - and then you are free to drop the users home directories.
Example smb.conf
[global]
workgroup = METRAN
encrypt passwords = yes
wins support = yes
log level = 1
max log size = 1000
read only = no
[homes]
browsable = no
map archive = yes
[test]
browsable = yes
read only = yes
path = /usr/local/samba/tmp
e.g. remove [homes] section