Here are a Few Turning Points That I Think Would Make a Difference
Simon Magus and Peter (approx 63 AD)
Simon Magus was a Samarian (Northern Israel) magician who, around 63 AD converted publicly to Christianity and was baptized. He was criticized by Peter for trying to monetize his own conversion.
The addition of a mere few words to the account recorded by Luke in Acts, (8:20) "...it's not your sorcery, but because you thought you could buy the gift of God with money..." would have help give clarity to church fathers when thinking about the subject.
The Murder of Hypatia (415 AD)
Hypatia was a popular Egyptian professor and a dedicated atheist (neoplatonist). Because of her popularity, church leaders approached her socially and for advice. Because of this, Hypatia became deeply involved in a internal political struggle within the church between her friend and recent convert Orestes (who was also the Roman prefect, or governor of Egypt) and the "rightful" heir
(people believed church leadership might be hereditary) Cyril. The entanglement got Hypatia murdered by a mob. Later historians would record her both as a witch and a saint.
If, instead, you had something like the O'Reily-Stwart Debates between Hypatia and someone, recorded by antiquarians. Both sides could walk away claiming victory. It might have made clearer for posterity contemporary atheist values (and distinguish them from "magic"), better define what witches or magic was, and maybe have saved Hypatia's life by convincing one of the two sides to back down.
King Phillip of France and the Betrayal of the Knights Templar (Friday October the 13th, 1307 AD)
What do you do when you owe a stupendous amount of money to the only international bank in the world, and you need a loan? Why, of course, you arrest the bankers, seize the bank, and approve your own loan request! King Phillip set the precedent for the convenient finding of "witches"; government searches as a cover story for property confiscation. The way in which this was done would be mirrored so closely by the Spanish Inquisition (1478) that we tend to think of these two events as simultaneous.
The Pope (the seat of the church was in France at the time) was a puppet of the French king, so it might have been too much to hope the Pope had took a public stand on defaming, torturing, and murdering the church bank. Edward II had just become king, and was too weak to take a stand -- but maybe he could have. Maybe if cynical historians had done a more thorough job of popularizing the money grab for what it was, instead of allowing the charges of witchcraft to linger, nor set the precedent for Spain that this way of doing business got results.
The Spanish Inquisition (1478)
Ferdinand and Isabella (the same pair of Columbus fame) were a pair of weak monarchs over an extremely divided Spain (7 kingdoms, 5 languages, and half-occupied by the Almohad Caliphate (empire) in the south). You know how we can unify all these people under our rule? We'll search out non-conformers and take their stuff! Worked for King Phillip, right? The Spanish Inquisition set our popular attitudes about magic and witches, despite it being largely a political land and property grab by too weak monarchs.
Again, bitter (and preserved) critique by historians would have helped keep attitudes in the present more level. Little known fact : Pope Sixtus tried to reign in the Inquisition from within. Maybe he could have publicly denounced them, instead. Or, maybe if the Pope had been really clever and suggested burning (instead of seizing) the belongings of witches, would have nipped the profiteering motive from Ferdinand and Isabella. Maybe Reformist attitudes could have matured early and denounced the action (Martin Luther would nail his theses to the wall in 49 years), with the protection of the German nation behind them.
Salem Witch Trials (1692 AD)
By now steeped in a lot of paid-for press making witches bad. It's possible these would have happened anyway -- there's thought that something medical that drove the people temporarily insane.
Maybe without the imaginative groundwork laid by the Spanish and French Inquisitions this insanity would have manifested as dragons in the New World? Maybe fairies? Would have resulted in, perhaps, a new myth, instead of the shameful memory.