I haven't had a chance to look at the OpenROV code, so I can speak to if its being used or not.
I have looked into using the BeagleBone PRU for another project though. My impression is the PRU is more for real-time communication. It doesn't have a multiply instruction and it's programmed in assembly, so it'd be kind of tough to build a controller in it.
The BeagleBone is pretty fast. If your autopilot were implemented in a reasonably fast language it'd probably be fast enough just running on top of regular Linux. You could try looking for real-time OSes that are ported to the BeagleBone.
For more information on PRU see these links: