Faster IO on ARM Cortex-M3 (Sam3x8e) than PIO_SODR and PIO_CODR?
I don't know the SAM3X family but the Atmel Studio IDE and the UC3 Family from Atmel.

Try adding the Clock Module to your project, configure it via the config_clock.h file, then add a sysclk_init() call to your main and it should be going a lot faster.

The SAM3X by default clocks at 4MHz if I'm not mistaken.