Hope this message doesn't come too late...what would I do? A quick disclaimer, though. All human beings are imperfect, and all police officers are human beings. Thus, all police officers are imperfect - some more imperfect than others.
To an extent, this question seems to focus on self protection from wrongful incrimination. When the situation is the word of high-ranking officer against a low-ranking one, the low-ranking officer could be SOL without good proof. In such case, I would recommend joining some form of police association, such as the Police Benevolent Assocation (PBA) or Fraternal Order of Police (FOP) http://www.sspba.org/ http://www.grandlodgefop.org/
I am not as familiar with rules of use and punishments for misuse of NCIC. Imagining the worse, your best bet would be to maintain that the individual using other's ID has the ability to do that. As I said before, that could become the junior officer's word against the senior officer's word - and if the junior officer is facing punishment in such a situation, having legal assistance becomes important. Try not to rock the boat, but don't let someone simply push you out of the boat without a fight, either.
Does that make sense?