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Telling a higher ranking officer you did not want to run, even if you subsequently did run, is still insubordination. As far as whether or not this will go to a trial or administrative sanctions that is up to the commander. Your commander can accept or reject the Article based on what is stated in the report, but even if she is the one who is involved in the action she can impose sanctions, that is not a conflict of interest.
Quite honestly, they could not prove any disrespect to the Officer if you did salute and issue the greeting. There is no way to prove any intent of disrespect for that, but for telling the NCO you did not want to run, they could prove disrespect/insubordination for simply that comment. Typically, it would be grounds for administrative not criminal sanctions, most usually a reprimand.
I would go sit with your local JAG, as is your right, if you believe this is being done as a pattern of harassment against you and discuss the matter with them, as they can go to the more senior command on your behalf to try to resolve the issue without you getting severe sanctions.
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