Generally speaking, if I have a raw SAM9x35, would it be possible to flash GHI firmware on it?

The reason is that a simpler board by omitting some peripherals still works for my project, but I like to have the micro-controller’s performance, and NetMF SDK for development.

If you want to license GHI Firmware you should contact GHI via Consulting services in Support section.
But may be Oberon has also a Firmware for your chip.