I agree, but latin was the language of the educated in Europe because of the (Catholic) church, and the universities pre-date the C of E by several hundred years.

I was going to answer with just "the church" but the OP specifically asked about academia.

It was the language of the educated because of the Roman Empire. The elites used to study how to be Roman elites before the 5th century, and when Rome fell they just continued, as it was the established sign of higher class. The elite has been educated by Cicero for the last 2 millennia, and continues to be so.

A good analogy is French being the language of the elite in Britain, well after the Normans got merged into the general population.