Ultimately it's the trainer's choice, but the trainers generally don't have the common sense that the viewers have. If you and I are having an official battle and I decide to use my crazy, violent, unruly Pokemon, then it's my decision and my fault if anything bad happens.
This makes me wonder how much power the Leagues have when it comes to making large rules like "No disobedient Pokemon in official battles/contests". They could make a rule like that, sure, but they don't seem to inspect the competing Pokemon beforehand so they wouldn't know that a trainer has a disobedient Pokemon until said trainer actually sends it out to compete. Disqualifying someone mid-battle for sending out a disobedient Pokemon would be unfair, but waiting until the damage is done would be too late.