Well.. don't serve the files in your ftp server. (you are not allowing remote users complete access right?)
Your remaining trouble will involve scp.
Why not keep the files in a location the user does not have access to, i.e. not in that users account, and have them use a script to execute the file? They can copy the script, but that doesn't do them any good.
Another issue is why you care that this user can copy your java files.