I agree. Seeds are trained to use magic as well... but they can't use it unless they have a junctioned GF!
Unless the GFS can be taken from under every stone of the road (we saw that is not the case! Getting GF's is a hard task!), the soldiers have a special abbility that seeds don't have! That is not logical from me.
Soldiers shouldn't use magic. As I said before, the right way to improve their abbilities should be higher physical attacks or weapon enhancement.