Precision timing using arduino and external clock
You can use an Arduino, but calibrate it to an external clock (or replace the clock with the external one). 

For instance Teensy 3.0 can use this FreqCount library https://www.pjrc.com/teensy/td_libs_FreqCount.html and basically compare its internal clock with an external one -- for 30 ppb, you'll need to average over 1 minute or so, but you can then calibrate your internal oscillator for basic timing. 

To keep things stable you'll need to ensure the temperature of the arduino's crystal doesn't change too quickly for the calibration to catch up.

Alternatively, use an arduino, and replace its crystal with an external OCXO signal.