As with anything, there are at least two sides to every story, and somewhere in the middle is the truth.
The original post says that they were "chanting/cheering for their teammates". Based on that statement alone, I don't see anything wrong with it. Based on that statement, there does not seem to be any taunting. The original post was about teammates cheering for teamates, and makes no mention of spectators that I saw, other than the ref commenting to one that he should have given them a yellow card, which in my opinion is inappropriate. The official does not need to respond to parents like that, he or she should address it with the coach or game management. When he or she says he should have done something in a situation like that, it causes more problems than it solves.
Al, while I see your point, I don't think it really addresses the issue that this post was about, unless you are including substitutes as spectators, which I don't think is correct. I do agree that the official has the right and the duty to control the game, but based on the information in the original post,(including the official's comment to a parent) it is hard to make the jump that there was anything excessive about the cheering, and I am led to believe that it was perhaps an inexperienced (or grumpy as HLinNC said) official going somewhat overboard.
But we do not know the official's side. Was there a request from the other team that the cheering/chanting be addressed? Or was it only the official that was distracted? Are there rules in place that address this situation? In high school football (at least in my area) we as officials can require the head coach of a team to quiet the marching band if they are playing during the snap count while the opposing team has the ball. Though this is not a perfect example, since the opposing coach has to request it and the band members are, in fact, spectators rather than participants or substitutes. (Not to mention, there isn't a snap count in soccer).
I would imagine that the cheering/chanting was at least encouraged by the adult spectators and perhaps coaches present, but from the information available, it did not seem mean-spirited. and they were cheering FOR their team rather than AGAINST the other. And again, this was directed at the substitutes cheering, not the spectators.
My suggestion would be to address this issue with the league or athletic association governing the game to see if there are rules that address it. Since the situation involved 9yr olds rather than older kids, there very well may be, in which case the official was well within his duty in his actions, but based on the information available, it does not sound like he handled it as effectively as he could or should have.