The tournament is supposed to find the best Professor, not the best player. Beating them at their own game? You make it sound like there is some grudge between the Professors and Players, when in fact I'm sure a lot of players are angry that this has happened, because they have respect for the effort that people put in to run tournaments and like to see them get a reward for it.
The person who got second deserved to win, and should be given the prizes and award. If you win Second Place, then that shows you were superior to everyone in that tournament aside from the winner, who shouldn't be counted.
The purpose of tournaments like this, and those similar to players, is to give something as a reward to a specific group of people. Would this make it OK for players to enter other countries Nationals and take the prize support from the local players, since they can beat them in a straight up game of Pokemon? Should it be OK for people to gatecrash Worlds provided they win some games, since they could beat them in a straight up game of Pokemon?