That's the point, discipline has nothing to do with running away, in fact almost the opposite. Morale dictates if a unit will rout, those spearmen obviously had low morale at the time of seeing the enemy. The discipline they have means that after they start fighting you can easily get them to disengage from the enemy, and that the won't charge without orders. It may also affect whether or not routing units that are undisciplined and not elite will scare them into routing or losing morale.