I think the TD made the right call. There are some comments in this thread that confuse the issue. First, this is not about teaching someone the rules. I'm sure the player in question knew you're supposed to shoot the cue ball first, so references to people not knowing the rules are just another way to insult APA rules. Second, ball-in-hand is a penalty, and can be applied to both fouls and to sportsmanship violations. Calling them sportsmanship fouls only confuses things. The shot was clearly not a foul under APA rules. Fouls are listed in the Team Manual. The question then becomes, how do you resolve the situation? First, the TD must decide intent and penalize accordingly. If it is determined that the player was trying to get some advantage by changing the layout of the table, the TD can penalize with ball-in-hand or stronger. Loss of game is possible, as is loss of match, as is disqualification from the tournament, even suspension from the APA. That part is up to the TD's (and LO's) discretion. If it was an innocent brain fart with no malintent, then all balls moved are considered moved by accident, and the game resumes with no penalty after the table is reset. To reset the table, the opponent replaces the balls where they were (if possible) and the original player shoots again. If replacement is determined to be impossible, then you terminate the game. In 8-Ball you start it over and the original breaker breaks. In 9-Ball you mark the remaining balls dead and the shooter who struck the 8-Ball breaks (though it's not likely in 9-Ball that you can't replace two balls).
Those are the rules. You don't have to agree with them, just abide by them if you play by them. There are many folks here who don't like the discretionary part, and that's ok, but it does shorten the Team Manual and soften the consequences of an honest mistake.