It's most definitely possible to control a stepper driver with the PRUs. Take a look here:
https://bitbucket.org/intelligentagent/replicape/src/2143a25b0537e6959e674441add9ee7866278049/firmware/firmware_00A3.p?at=master
In just the same way as the AVR MCUs can output step/direction to GPIOs, so too can the PRUs.
EDIT: Just found another BeagleBone project that does this: https://github.com/modmaker/BeBoPr/wiki/Hard-real-time-stepping
EDIT2: Another link explaing the Replicape approach http://hipstercircuits.com/pypruss-a-simple-pru-python-binding-for-beaglebone/
https://bitbucket.org/intelligentagent/replicape/src/2143a25b0537e6959e674441add9ee7866278049/firmware/firmware_00A3.p?at=master
In just the same way as the AVR MCUs can output step/direction to GPIOs, so too can the PRUs.
EDIT: Just found another BeagleBone project that does this: https://github.com/modmaker/BeBoPr/wiki/Hard-real-time-stepping
EDIT2: Another link explaing the Replicape approach http://hipstercircuits.com/pypruss-a-simple-pru-python-binding-for-beaglebone/