I do not have an answer to the dilemma. But I do note that the efforts of schools and parents to control the friends of their student/child are nearly always wasted. Having made many observations, what typically happens is that the kid simply takes the friendships underground, where there will be the same amount of companionship, just without getting caught. It is sad that parents and mechanchim are subject to the delusion that their efforts are accomplishing something while they are completely futile.
In fact, the range of restrictions placed on adolescents is extreme, and few, if any, are successful ingredients of chinuch. In reality, one who works on helping the kids see the beauty of following mitzvos, appreciating Shabbos, davening, learning, etc., is far more likely to produce a happy child who stays “on the derech”. The rod spoils here, and the obsession with discipline is fruitless pathology.