Might try this:
Create an FTP/scp accessbile folder (xfer) outside of Moodle ... another web server or a directory on the same server as the Moodle.
Upload the files to /xfer via FTP/scp or however one transfers files. Might make note of the full URL to get to a file:
Might upload a zip and unzip it in the /xfer folder.
Setup a URL uploader repository in your Moodle. Then, while in Moodle, use the URL uploader and point to file/files (folder?) in the http://somesite/xfer site.
There might be some issues related to files that are updated in the xfer folder as once in Moodle 2's filedir area and database has a reference to them. Moodle won't autoupdate information contained in the DB - change to a filename and size might cause errors in Moodle but only way to know for sure is to 'tinker' with a few files/folders and see! ;)
'spirit of sharing', Ken