That said, America (via Trump) has yet to fully regain control of our intel agencies... the number of deep state crooks embedded throughout the agencies is still far higher than the number of honest people. It's just going to take more time to wrestle control of the agencies away from the evil forces of the Clinton/Bush/Obama/Soros/etc. organization.
I don't know what the rules/laws say about firing non-political employees are, but if Trump wants to drain the swamp, that's where to start. All the federal intel/leo agencies are now under the authority of the Department of Homeland Security (DHS). The DHS answers to the Executive Branch.
That said, I'm confident there are many patriotic dedicated personnel in the FBI, CIA, DIA, NSA, etc. who help keep us safe from muslim crazies. I thank them for their service.