I've looked around a bit online, and apparently it is possible to run a samba server under a non-root account, but the port it listens on has to be above 1024. After a quick look, the only way I saw to get a Windows machine to access a different port is to map port 139 to the new one using ssh tunneling. The process is pretty involved, and needs putty installed on the system. If you have putty installed, then you might as well use it to copy files over to the reader's sshd server.
Anyway, I'm willing to give someone a hand building samba for the PocketBook Pro devices if they want to pursue this, but I don't use Windows much myself, so I wouldn't want to do the bulk of the work.