Any inventory of the traces of Latin in Western civilization has to start with school. Until the 1960s the world of education was closely associated with Latin, when not actually confounded with it.
What does "when not actually confounded with it" mean?
It probably means that everything that had to do with receiving a good education in the past was in Latin. Latin was considered the most important and educated of the languages so I think the paragraph is suggesting that education was so closely related to Latin that could be considered as the same thing.