The Muslim Brotherhood has survived for 85 years despite being formally illegal for much of that time, including the entire period 1954-2011, though it elected members of Parliament (as independents) in the late Mubarak years. Before Nasser's 1954 crackdown the British instigated a ban in 1942 during World War II and the King banned it again in 1948. In other words, Egyptian secularists who feel that today's court decision, which "bans the activities of the Muslim Brotherhood organization and its non-governmental organization and all the activities that it participates in and any organization derived from it," will mean the decisive end of the organization are unlikely to be proven right.
Even without the history of the Brotherhood as a tightly organized underground body which has survived for decades in the shadows, today's decision will be appealed. The case, in fact, was not brought by the government but by the leftist Tagammu‘ Party.
Nor is it made clear in the decision whether "any organization derived from it" includes the Freedom and Justice Party, the Brotherhood's political wing. If the FJP is banned from running in Parliamentary elections, the Brotherhood will have no incentive to try to find a modus vivendi with the military backed government. Up to now some have speculated the FJP may be allowed to run candidates, and today's ruling is unclear on the fate of the FJP.