Bill Gertz has more on the termination of Stephen Coughlin here, while Steven Emerson reveals how grave the story really is during an interview on Hannity and Colmes in which he describes the motivation for Coughlin's removal this way:

[Coughlin] had offended a top aide to the deputy secretary of defense, Gordon England, whose aide, Hesham Islam, I believe is an Islamist with a pro-Muslim Brotherhood bent who has brought in groups to the Pentagon who have been unindicted co-conspirators.