Then, books on deism existed in the libraries of prominent colleges like Yale and Harvard. The ideas were spreading and the then "orthodox" leaders of those prominent educational institutions had to react to a such system that conflicted with "orthodoxy."
How did the "religiously correct" orthodox Protestants deal with the problem of their libraries having books on deism which influenced students in undesirable ways? That's the controversy. Below is what Stiles said:
It is true with this Liberty [of accepting deistical books into religiously-affiliated university libraries] Error may be introduced; but turn the Tables [and see that] the propagation of Truth may be extinguished [if you do otherwise]. Deism has got such Head in this Age of Licentious Liberty, that it would be in vain to try to stop it by hiding the Deistical Writings: and the only Way left to conquer & demolish it, is to come forth into the open Field & Dispute this matter on even Footing—the Evidences of Revelation in my opinion are nearly as demonstrative as Newton’s Principia, & these are the Weapons to be used . . . . Truth & this alone being our Aim in fact, open, frank & generous we shall avoid the very appearance of Evil.Stiles was a good classically liberal Whig. He might have handled the circumstances with more liberality than say, Timothy Dwight, the President of Yale who succeeded Stiles. Stiles was, if I'm not mistaken, more sympathetic to Jefferson's and Madison's Democratic-Republican party than the Federalists. In fact, Stiles was a Francophile who supported some of the excesses of the French Revolutionaries.
Stiles was actually one of the "orthodox" figures that heterodox men like Ben Franklin felt somewhat comfortable sharing their religious heterodoxy with. The same can't be said of Timothy Dwight who was less liberal than Stiles.