Actually God teaches that it is good to teach children obedience and respect. In fact, the ten commandments require it and the teachers are representatives of the parents. Besides being against the laws of God, if you let your children think you will support them in their disobedience you are asking for big trouble, way beyond a slight inconvenience of sitting where they want.
Failure to teach children the difference between true, objective right & wrong (from God) and the fallible man-made version borders on child abuse. Those who say "rules are rules" without regard to the legitimacy of those rules wallow in moral relativism, without even knowing it.