Tillerson got rid of many political appointees but these career civil service bureaucrats are almost impossible to dislodge. many left in disgust, which was at least something good; but the rest will have to be flushed out with flame throwers, like Japanese dead Enders on Okinawa.
You are right. The entrenched “civil servants” are nearly impossible to dislodge. However, these resisters can be reassigned and moved around to jobs they might not find to their liking. The resisters can do a lot of damage if left in places where they can thwart the will of a president.