This is what RetroLink and Retro-Bit N64 USB adapters do, because they don't adhere to the USB HID standard.
I posted a couple of possible userspace drivers here https://www.reddit.com/r/RetroPie/comments/53bt1d/retrobit_aka_retrolink_usb_adapter_driver/ but nobody has reported trying them out yet.
Alternately, get a different adapter. I have had success with one which looks like this: http://i.imgur.com/cC8iegW.jpg