One has to be nuanced on the Muslim Brotherhood—many/most of them are, in Islamist terms, relative moderates, and the (largest) Egyptian branch long ago abandoned violence as a means of bringing about regime change (favoring instead social activities peaceful political participation). The same is true of the MB in Jordan, who also participate in the electoral process. Indeed, both the Egyptian MB and the Jordanian MB/IAF continue to play by the constitutional rules, even though both governments take various non-democratic measures against them.

As davidbfpo correctly notes, the UK MB were instrumental in taking over and deradicalizing London's notorious Finsbury Park mosque, in not-so-secret cooperation with the Metropolitan Police.

The MB, however, are no fans of US foreign policy. I think this is the real dilemma: not how Washington deals with small, radical anti-democratic anti-American Islamist groups—the al-Qa'idas of this world, as important as they are—but how it deals with genuinely popular, semi-democratic, less radical groups that oppose US policies or interests.