Islamist fighters including Ansar al-Sharia were blamed for the killings at a U.S. diplomatic compound in 2012.
Public demonstrations, a Libyan military strongman and defections to ISIS have all damaged Ansar al-Sharia's standing in Libya.
The aircraft crashed over a residential area as it returned from bombing raids over Derna.
The military government said they imposed the ban to prevent Libyans joining terrorist groups abroad.
Libya's eastern authority has banned women under 60 years old from traveling alone.