Sounds like more of a mod conflict, yeah. There are instructions on the RwF page about reporting issues like this, along with logs. Glad it's been working out for you, with Mac, since I have no idea about any of the differences between PC and Mac versions.
Great Theologians are just meant to, conceptually, give a level of prominence that religion and religious figures have played beyond the mere founding of a religion, and, mechanically, to make Great Prophet Points more on par with other Great People Points.
The short of it is that Great Theologians are generated with Great Prophet Points after you have founded a Religion or after all Religions have been founded (i.e. after Great Prophet Points become useless in themselves).