The purpose of civil service reform was to end patronage, not to insulate the civil service from political supervision. The idea was to have well-credentialed employees, instead of political donors, carrying out the policies of the elected President. It was not to have employees exercising power independently of the policies of the President.
The Pendleton Civil Service Reform Act was enacted in 1883. Four decades later, former President Taft wrote Myers v. United States, which still reflected the conventional view that the President was actually in charge of the executive branch.