As an FO, I had an incident similar to this during my first year. To make a long story short, I stomped on the brakes to keep a Captain from taxiing onto an active runway, without a clearance, just as a Citation was crossing the fence. The Captain had the gall to begin chewing me out for touching 'his brakes'. I silently took this one sided dialogue for the duration of the short flight until we arrived back in the hub. Once the shutdown check was completed, a whole different conversation began; one initiated by me.
Though it felt good to speak my mind to this individual, (FWIW, he was exceptionally polite to me for the rest of the trip), I was the one who screwed up. In my desire to go along to get along, I finished the trip, went home, and told no one.
What I should have done was leave the trip, report to the CP, and make sure the A/C was powered off so as to save the CVR. Though I didn't know that it existed as a resource at the time, If I had to do the same situation over again, I would have been in touch with our Pro Stands folks as well.
I received no, zero, zilch, nada in the way of training from my company on what do do in this situation.
In this particular case, the situation has solved itself in that the former Captain no longer works for our airline. In fact, to the best of my knowledge, he is no longer involved in Aviation.