No, hiring is largely done by other civil service personnel. The Secretary of State isn't deciding who works in the cafeteria - there's a number of tiers of career employees between him and that decision.
I dearly hope the janitor isn't the person who the grousing about the deep state is targeted at... Because if that's the case, it's a pretty weak one.
The janitor isn't the reason the DoS makes poor decisions. These decisions are made much higher up the food chain, and elected officials have direct influence over the people who make them.
