FreeRTOS for Due, Teensy 3.0 and AVR Arduinos

You can totally takeover the SysTick interrupt. The plan is to have a weak symbol for

int SysTickHook();

This function is called before the Arduino part and will only execute the Arduino code if you return zero.

This doesn't solve the problem of two libraries wanting direct access to SysTick but that is what RTOSs should do.