No question that I agree with your sentiment entirely. But that does not mean that "company procedure" always needs to trump judgement. It does not, and the legal basis for that assertion is quite clear.
Case in point: June 12, 1972. American Airlines Flight 96, ORD-LAX. A DC-10. We all know the story, and the "eternity" that ensued. In analyzing the crash, the invesitgaots determined that the Captain followed procedure extremely well. Unfortunately, hanging on to the prescribed airspeed after the engine loss did not allow him to maintain control. In simulator re-enactments, the "sloppy" pilots who let the airspeed increase flew out of the event and landed successfully.
Sure, cases like this are (thankfully) rare exceptions to the rule, and procedure will almost always be the best course of action. But this profession can sometimes benefit from experience and judgement of the pilots who are actually flying the airplanes, rather than the engineers who are designing them and the procedures.
Someone HAS to be in charge. Someone's judgement MUST prevail over all others. The law makes that determination, and makes it very clearly.