“Reason and free inquiry are the only effective agents against error. Give a loose to them, they will support the true religion by bringing every false one to their tribunal, to the test of their investigation. They are the natural enemies of error and error only. Had not the Roman government permitted free inquiry, Christianity could never have been introduced. Had not free inquiry been indulged at the era of the Reformation, the corruption of Christianity could not have been purged away.”

Reason and free inquiry are effective agents against error but, not the only agents. True knowledge for one (knowledge based on the premise that there can be no true knowledge of a falsehood, it is either an absolute fact, or it is a falsehood - no matter the claim to knowledge) is an effective agent against error. By way of example, the knowledge of simple math; if I have 2 apples in one hand and 2 oranges in the other, I have 4 fruit. Such knowledge is an effective agent against error. If there be an absolute knowledge of the Christ as He truly is, that can not be shared through reason and free inquiry alone. Reason and free inquiry have not yet purged away or, eradicated the corruption of Christianity (but added to it).

As much as I admire Jefferson, I'd have to say the only reason the Romans ceased persecuting Christians and adopted the church was in an effort to exert more control.

That I believe.