It runs a similar risk to most other functions of the bot. There have been those who have been banned for rotation only. Blizzard has also shut down many honorbuddy competitors who's bots are only combat rotation only.
Third party program is a third party program. Also keep in mind that if you suddenly start out damaging the other person in your guild who plays your class, they may ask questions. If you don't understand your rotation enough to the person to explain why or how you suddenly went from doing less damage than them to significantly more. It could cause suspicion..