Plato's Academy definitely did not start as a mosque... So I guess you're refering to al-Qarawiyyin University.

Islam did a much better job of incorporating science, so it's not really comparable to a seminary either. It's not like they only taught theology there. We owe a great deal to the science being done by Muslims in those days. A hell of a lot more happened there than in the Middle Ages in Europe.

Besides, the university of Cambridge also started as a religious institution. I see no difference. All old universities have religious roots I guess? It took a long time for mankind to come up with secular education so why are the Islamic roots even a cause to question the validity of this university?