Hide from whom? Why don't you save it inside a protected directory (owned by root:root and with 750 permissions)
The file squid.conf is usually stored under /etc/squid, so making the permissions in that directory be 750, would make the files in that directory only accessible to user and group root. Would that be enough for you?
You might need to make the directory group owner be squid, so that the user that finally runs the services can access it, but that depends on how you have configured it.
Hope that helps,
Pedro.