We believe that disabling ftp will cost customers, and will definitely increase calls to support, as standard functionality, that folk are used to, won't work.
Though ftp passwords are sent in cleartext there are a lot of protections built into ftp (such as user jails) that aren't in ssh.
ssh should already be running on all DA servers, but to make it work you have to give users a real shell, that they can then use to log into your server.
Once logged in they can see lots of files you may not want them to see, including the /etc/passwd file, for example.
Using only the file manager will keep a lot of users from uploading large files.
And the file manager doesn't convert line endings when uploading files, so .pl and .cgi files may not work as expected.
Jeff