What is it that you are trying to do? Just transfer certain files from one known user to another? Doing remote Web-based administration where you want passwords to be encrypted (very good idea, by the way)? E-Commerce?
Apache can be made secure, using mod_ssl. In fact, unless I'm mistaken, OSX's Apache comes with mod_ssl; it's just a matter of setting it up right. If it's not there, you should be able to get it from the Apache Website or, failing that, Freshmeat.
If you're looking for something FTP-like, I'd use scp myself. This too comes with OSX, as part of the SSH package.
Oh, and yes, you can run a secure and non-secure server on the same machine. It's a matter of setting up two virtual servers for Apache; Webmin can help you do this. Set one to use mod_ssl for everything and the other not to use it.