I'll premise this by stating that one of the principal differences between Reverend El Shafie and me is that I'm a lawyer, so my understanding of the definition of a terrorist organization might be different from his.
To my knowledge, the Muslim Brotherhood has never been categorized as a terrorist group by a western nation, and would therefore land outside of that definition. The Muslim Brotherhood, however, is a political expression that is, by their own admission, tied to a more extreme expression of Islam than the understood majority of the population of Egypt.