I get what you’re saying, but in reality this isn’t always possible. If you are directed to do something by your superior and you choose not to comply, disciplinary procedures will start, and will ultimately lead to your termination. Throughout that process, the principled protest that lead to your termination would be muddied and probably forgotten. Resigning on idealistic or principled grounds sends a stronger message than allowing yourself to be fired, and least for those in the administrative state that don’t have highly visible jobs. The result is still the same either way: the action you were protesting was probably carried out anyway by someone less principled than you, but you’re out of a job and few people will ever know why.

If you loudly resign, your message will be received by more people and will be backed and strengthened by your sacrifice. It’s fucked up that it has to go down this way, but when there are two bad choices I’m glad enough people are making the harder one that might benefit more people even at personal expense. For heads of agencies and high level staff it might be more impactful to let yourself get fired, but I think those cases will be the exception (the FBI director, for example, should have let himself get fired).