Although the Due is supposed to give you 1Msps, when you go through the whole stack to make it work it actually margins at 25ksps. There is way (http://arduino.cc/forum/index.php/topic,6549.0.html
) for the AVR MCU's to reach faster ADC's but since the Due is based on an ARM architecture, the same won't work. I'm reading the application note (http://www.atmel.com/Images/doc11106.pdf
) to figure it out but I'd be happy to hear from you on whether or not you could reach a solution.
Someone has posted a similar lower level code in another thread (http://arduino.cc/forum/index.php/topic,137635.0.html