I had to "fire" ac couple who worked for me and it was a lengthy chore that required documentation leading up to the decision with all the i's dotted and t's crossed. While you don't want it easy for a supervisor/commander to just get rid of someone for spite, there should be a cleaner route for when it can be justified. Congress can do that.
The civil service act has been around a long enough time that no one will accept its upending. It has a good purpose. Leave it alone