The problem is loss of control once a bocher enters the army he is no longer under the direct control of his rav/yeshiva but an 19 year old officer, his place of learning looses the income his presence brought
the biggest fear is not those who are not suited for full time study will discover a different world and values. But that the best students will leave the yeshiva and become useful citizens by serving in the army and entering the economic life bringing an end to the cycle of poverty controlled by the yeshiva world.