Just because Wray was appointed by Trump does not mean the FBI operated at the whims of Trump. For one, these positions are merely nominated by the president. They still have to be confirmed by the senate. The president is effectively given a list of people from whom he can nominate. There is also strong institutional inertia here.
A lot of people get strong armed by the FBI. They hold a lot of power. This is not conspiracy territory either. There are congressional oversight committees, but their ability to use classified information gives them a lot of leverage.