Civil servants use their personal judgment 100% of the time because they're tasked with bringing local context to decisions made elsewhere. 99% of the time this isn't a problem because most of the people involved understand the process and their role in it.
The Republic is designed to protect and preserve the rights of its citizens. That government workers have consciences is a feature, not a bug.
The machinery of the American state is built on the voluntary cooperation of millions of Americans. Trump is not entitled to that; he is not a king and that's not how we do things here.
If he wants to gut the government and be ruler of the ashes, he may do that. If he wants to be the most powerful man in the world, he must earn the cooperation of the civil service.
While I sort of agree, there is also the very real threat of retaliation that could severely damage or destroy person's life. Both Trump and Musk are known to be very vindictive, and have both massive power and money. I'm not really sure what I would do when presented that kind of choice.
Obviously though, it’s the dirty hands problem. 99% of the time we don’t want civil servants to do this because 99% of the time the President isn’t actively trying to unmake the Constitutional order. It’s very problematic to have civil servants thinking their judgement should overrule their leadership, but we’re in extraordinary times and there is no leadership of an opposition movement that can coordinate to set any sort of guardrails around that kind of willful insubordination.