An atheist is not a threat to JW hive minds. The idea that Jehovah does not exist is preposterous, and cannot be proven. The limited logical reasoning skills and lack of knowledge of fallacies and biases make the average JW (and any other theist) immune to the argument 'there is no compelling reason to believe in gods'.
A (God believing) exJW who doesn't believe the GB anymore most likely has arguments and evidence that strongly support his position. JW might be swayed (but unfortunately not nearly often enough). These people are a threat to the GB themselves, and they need to be eradicated.
In addition, the atheist exjw generally doesn't care what others believe (although they might not like cults like JW much) and thus don't feel the need to preach their position to JW (and get themselves DFed in the process).
The still believing GB-denier is likely convinced that JW are sincere but misguided, and need to be saved from their false religion in other to gain divine salvation. These exjw are more likely to preach to JW (and get themselves DFed in the process).
Anecdotal evidence: I'm a known atheist exjw who hasn't been DFed :-)