So, let's summarize: She got in trouble not because she wore a special running suit to cover her body, but because said running suit was two colors, not one, as existing rules state. If she had worn the exact same suit, but died it a single color, there would be no violation and no problem.
So, then, here is the question. What is the purpose of the rule? Why is it important that this rule be followed? Was the rule put in place because other teams had had uniform violations that, for example, created confusion in a track meet about keeping track of people? Here, we know that the rule had not been enforced for the past 3 years; therefore, we know it is not a critical rule, because her uniform confers no advantage. And we know that she is a Muslim, and is wearing this uniform in order to preserve modesty as her religion requires. So, the officical could have done any number of things: He could have allowed her to run and provided a warning for future meets (given she was there and ready to perform), he could have DQed her knowing full well that he would ignite a controversy that cannot reflect well on anyone involved; he could have simply allowed her to run and end of story. He selected the one that created the most havoc. Yes, he asked her to abide by the rules; yes, she did not handle it well. Yes, the coach made a mistake. But I just don't see a major problem in letting the issue pass, and simply making hte coach aware. This would be similar to telling an orthodox Jew that he has to remove his headcovering. You can do it, but should you? Some common sense all around would have saved the day.
It is disheartening to read all the responses. Everyone here who says rules are rules and must be followed knows full well that often they are not, and often they break rules and expect to get away with it, whatever the rule is. When a cop pulls you over for speeding, he can ticket you or give you a warning; that is a decision the cop makes. I'm going to bet you would want him to give you the warning, all you "let's follow the rules" people. That is no different here, with what the offical did. He had discretion and exercised in a way that ended causing a problem for a whole lot of people, that ended up being much more than what it was and that reflected poorly on everyone involved. This all could have been avoided.