It's not using authorize.net as a middle man at all. It's using the authorize.net gateway code to process transactions with EPN, as EPN uses the same methods as authorize.net.
Every authorize.net gateway set-up points the user to a secure server to finish the transaction process. All one has to do, as stated above, is replace the authorize.net URL with the EPN url, and voila.
I've never really used eJunkie but I can tell you that if you don't have FTP access to all of your shops files, you're not going to be able to get this to work on your own. You will need to contact someone higher up and see if they can do it for you. The authorize.net module they are using COULD be a shared module among all eJunkie users, which might make the change impossible.
Switch to zencart. lulz.