I have summarized the role of the political officers in the Red Army in this thread, so I'll allow myself to not repeat that information here.

Using the information that were presented in the above entry, the situation presented in the original question could have really arisen only between 22nd June 1941 and 9th October 1942, ast after the latter date, political officers were relegated to chiefly political affairs (morale, education, political awareness) and basically lost all their influence on the military issues. But in the period mentioned above, such officers or war commissars could interfere in the process of order execution. But according to the order no. 0178 of 1937, the loyalty of soldiers was not divided in any way as the differences of the opinion between commanding officer and a war commissar was not a kind of stalemate that could have been resolved by personal traits. If a situation case warranted interaction, commissar could have arrested the officer, temporarily depriving him of command and then take his position himself, with soldiers expected to follow his lead.

So, to sum it up, until 9th October 1942, war commissar could have simply taken the position of the commanding officer, and after that date, he could have really done nothing except informing officer's superior of the perceived transgressions.