I agree with the above, the runes and symbols are arcane and of a much older origin than the Schools or Colleges them self, and naturally, they will use them, just like most of the religions of our own world have been adopting both symbolicm, sacred places and buildings, to make the transition to the "new" religion easier.
I would keep them, if you can justify that there have been arcane activities in the keep, wich I assume that you want to do.
There are absolutely more people around like your self, for instance, our Warhammer RPG group is very very very rigid in its Warhammer Old World lore, and nothing new is allowed to seep in to it what so ever, unless, it can be really justified by means of tying it to the old RPG lore.