I don’t even go here, but I want the 10k comedy of errors that leads to and from this point.

LOL

I realize that you probably meant this rhetorically, BUT I’m gonna tell myself a story about how this would go anyway: 

So the Pope would throw an absolute fit at the idea of Cesare’s assassin having congress with his precious daughter (who was just about to receive an offer of marriage from the Duke of Ferrara! The timing could not be worse!), and so he’d demand that Cesare either fire Micheletto or kill Micheletto. 

What Cesare actually does is get Micheletto out of Rome by promoting him. No longer an assassin-manservant, Micheletto is now a reluctant general of the papal armies. Cesare and Micheletto go tramping gleefully around the Romagna carving out new territory, and instead of demanding  new states for himself, Cesare cooly demands a barony for his loyal general. 

Baron Corella can have an affair with the Lady Lucrezia Borgia, even if His Holiness still doesn’t approve. 

AT THIS POINT Cesare and Micheletto return to Rome, where under the Pope’s disapproving eye Cesare and Lucrezia have to turn an illiterate murderer into a grudging, bitter courtier, at which point they UNDOUBTEDLY engage in more and more complex not-quite threesomes: 

-Cesare and Lucrezia hide their affair by pretending that Lucrezia and Micheletto are continuing their affair, which means that the entire Vatican wanders around like “what does the Lady Lucrezia–who famously chose her last husband because he was ‘sweet as apples’–see in this dead-eyed torturer with his peasant accent and his utter lack of graces?” 
-Lucrezia starts publicly showering Micheletto with affection, partially to keep up the facade and partially to goad Cesare, who is super jealous
-Cesare and Micheletto have super passionate sparring sessions that end with Cesare’s blade at Micheletto’s throat and intense prolongued eye contact and heavy panting and Micheletto arching ever so slightly into the metal 
-Micheletto very carefully reminds Cesare that he is into dudes, only dudes, just dudes 
-Cesare somehow ends up sucking Micheletto off in a confessional as a way to restore his wounded masculinity??? by proving that Micheletto IS more into him than he is into Lucrezia
-Lucrezia poisons a man with Micheletto’s help, which makes Cesare even more jealous
-threesomes with Extremely Complicated Rules emerge

eventually the pope decides Lucrezia has to marry Micheletto, which SHOULD solve all of their problems but winds up causing fifty more.