> Even in Linux if you access the Pi's GPIO registers directly you can toggle pins in a tight loop at around 1-2mhz.

Careful, this is strongly dependent upon the hardware, not Linux.

I seem to recall that people doing SWD programming can barely get the GPIO's to move faster than a couple of KHz.

I can tell you that, at least on the BeagleBone Black, you have to do some Linux driver voodoo to get better than a couple of KHz.

Edit: I stand corrected. Apparently the Broadcom chip in the RPi does much better than the TI one in the BeagleBone Black when driving baseline GPIO's.