I suggest it is there for the following reasons:
Light - People read in libraries and write at Universities, studying requires reading and writing and reading and writing require light. Candles and fires are expensive and provide little light so during the day you want maximum daylight to save on candles.
Energy - You say 'Magic is transformation of energy' and what is a free source of practically limitless energy? Light/heat energy from the sun of course. If the glass is angled/curved correctly it could focus the suns light and heat in order to provide large amounts of energy to be used in magical erase arch projects.
Heating - Greenhouses are warm due to being made of glass. The glass in your temple will materially warm up the inside. In Africa this may be a disadvantage due to the heat outside already being high but you could remove the disadvantage by opening the doors/windows. If the climate got colder though this glass temple would remain warmer than the surroundings so it might be a useful thing at night.