I’m stunned at how often questions like this come up. They indicate a truly abysmal knowledge of the structure and purpose of the military. In theory, orders are either lawful or unlawful, the latter meaning illegal and unenforceable. If a soldier knowingly follows an unlawful order, and the order results in an illegal act, the soldier may well become subject to punishment as the participant in a crime. In the case you ask about, that would be murder or attempted murder and a slew of other charger enhancers. Ditto for the not-long-to-be-commander.
The “or” part of this, i.e. “disrespect” the commander should have nothing to do with this. The or would be “disobey.”
I cannot speak for third world countries or militaries that are not controlled by a civilian government, but for modern western militaries the next question would be this: is the soldier sure the civilian is innocent? Is the soldier sure the command is lawful, i.e. shooting the civilian is appropriate given the context and alleged violation foe which the order is being given?
Since you specified the civilian was innocent, and left everything else up in the air, the answer depends on the soldier, the military, what you define as a ‘commander”. and the circumstances, and what “innnocent” means.
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