Hi Kimberly
My lo used to wake up halfway through her morning nap doing a poo almost every other day. I would do exactly what you do- wait to see if she went back to sleep and if not, get her up. She was always happy and didn't seem to suffer from having a short nap, we just had to adjust timings for the rest of the day, sometimes she would last till bed ok and sometimes we had an early night.
hth
kathryn x