When hosting scripts and data on millisecond.com, there would only be extra security if you also encrypt the script itself. A person would still be able to download the script anonymously as you describe, but would not be able to read its contents.
Ultimately, though, the script has to be decrypted at some point and be available in plain text in order to run. I.e., a motivated attacker would be able to "participate" in the experiment and dump the decrypted contents on her/his system to obtain any (FTP etc.) passwords contained in the script.
Encrypting data files can be useful if you want to transmit them somewhere else, but there's no transport-layer encryption available to you (FTP, plain HTTP).