A What If Speculation
According to Ex Urbe, Pope Julius II was able to bring peace to central Italy by being a treacherous deceiver:
I'm not sure that the virtuous outcome would have been that bad. The obvious prediction from a man of faith would be that God would strike down Cesare Borgia. In hindsight, we can see that was quite likely. Borgia was already disfigured by syphilis and would probably die a year or two later, leaving a disgusting corpse. One effect: Machiavelli writes The Prince but includes the easily observable fact that God strikes down evil princes just when they seemed most secure.
Outcome if Julius II had been virtuous:
Julius seals his pact with Cesare. After his election, he continues to treat Cesare as a close ally, allows him to control the papal army, and use it to continue waging war in central and northern Italy. Thousands if not tens of thousands die in combat and more from bandits and disease as the chaos continues. Cesare secures Romagna and the papal states, then turns on Florence, probably Modena and Ferrara too, on the Venetian land empire, shoring himself up more and more at the cost of chaos. In the end either the Emperor invades to check Cesare's rise, or Cesare grows strong enough to make his bid to be Julius' successor, and bloody civil war erupts whether Cesare wins or loses as he and the rest of Italy battle to see whether or not the papacy will indeed become a hereditary monarchy. Death toll: tens if not hundreds of thousands.
Outcome if Julius II is a treacherous deceiver:
Cesare is instantly removed. The wars in central Italy cease. The suddenness of the change makes it easy for provincial forces, as well as papal forces and city forces, to bring about some degree of stability. The shock of the suddenness of Julius' betrayal makes everyone else wary of causing trouble. Peace is instantly restored, the Borgia Kingdom eliminated, exiles restored, Florence protected. Death toll: Cesare Borgia, plus, perhaps, a few of his guards and associates.
I'm not sure what effect that episode would have on the Protestant Reformation, which was just around the corner ….