The real problem here is the difficulty in fulfilling the need to have monasteries phased out, have schools phased in, and, probably most importantly for the sake of game balance, avoid "sweet spots" where both can be had for maximal benefit.
Now, the issue here stems from an inability to have technologies partially obsolete buildings, that they may be phased out over time, rather than immediately. Fixing this is a bit of a problem, and the only obvious solution requires a fair bit more paperwork than might be ideal, and it can't quite handle all the things which we might want from it, but in the case of something as important as education, the paperwork might be worth it, and the restrictions might still be better than the alternative.
I have only recently come back to Civ4, and have thus forgotten most of what there is to know about the restrictions of modding, but might it be possible to have a series of national wonders created, that then bestow benefits upon buildings of a particular kind? These could be introduced gradually, that buildings then improve much in the manner of current building chains, and could be obsoleted similarly gradually, as to phase out this "outdated" mode of education, without rendering it completely useless with one fell swoop. They would - again, should it prove to be possible (I willingly admit that I do not recall at current time if it is possible to have national wonders influence the boni granted by individual buildings) - represent nation-wide improvements to the educational system, which should, by their nature, have a roughly even effect on schools across the state.
Of course, if it isn't possible, then I suspect there is little to do but grit our teeth, mutter a prayer of farewell to sweet Hecate, and wave our monasteries goodbye as we enter a new world of alternative enlightenment.