Sure,
Don't allow root to log in remotely except through a secure,
encrypted app. (SSH)
Normal users can login just fine w/out deleting anything.
Use a privileged account and an ftp daemon which allows some
flexibility (like proftpd, but all of them have problems)
in configuration and only allow user logins(no anonymous).
If you are worried about security, you should think seriously about replacing anything that sends passwords
in plain text over the wire.