Are children like Pavlov's dog?

The quick answer is probably yes.  I don't think we can say that humans do things automatically in the strictest sense.  Skinner (1968) conditioned pigeons and mice to do certain routines in order to get food.  Yes, we do need to condition behaviour in the classroom and each subject has different rules that need to be followed, for example, rules in an art class are different to rules in a geography or maths class.  This conditioning is done so that teaching can occur in an atmosphere that is not chaotic.  So, we do condition behaviour, but it is not just a stimulus-responce method.  Children do actually think about what they need to do in order to conform to the teacher's way of doing things.  They know that one teacher is strict about standing up when another teacher walks in and that another teacher is more relaxed about it.  School, as well as the outside world, has a certain set of rules and children must learn how the system works so that they can fit into society.