You could probably update rockbox via the SD card as well. Theres semiworking USB support in rockbox if you compile a build with it enabled, but its really better to fix the OF.
Using manufacturing mode is relatively safe, it doesn't actually change the contents of your flash, just loads the Sansa firmware into RAM and runs it from there, hopefully letting you into disk mode so you can fix the flash. So basically you'd load the OF's recovery mode into RAM from a known good copy, run it, mount the recovery mode 16MB disk on your PC, and then copy a new (working) firmware over to it. Assuming the problem is a corrupted firmware thats preventing the builtin recovery mode code from working, this should work.