Yes, take the full two-week course, to maximize the chances that you’ll be done with this for a good long while. No one in their right mind “likes” taking antibiotics, but it’s best, if you can, to employ your rational mind instead of your emotional one in these cases. If antibiotics are that upsetting you might want to consider starting a good bacterial probiotic to (possibly) reduce the likelihood of future pouchitis episodes. The best ones are expensive, though. Good luck!