It's good that TV dramas have become more complex and ambiguous, particularly with regards to morality. But there is a tendency for them to lose any moral compass in their eagerness to show us the dark sides of the characters with whom they want us to empathize and to care about.
The Borgias wants us to follow Cesare's career with sympathy, but also shows him having people tortured into madness. What is the show's position on this? Oddly, it tries to whitewash him even as it revels in his dark side. It makes his victims into rapists and murderers. It depicts him as personally involved in tormenting Savonarola, but makes Savonarola a fanatic (of course) and a vicious homophobe. Now, it's true that Savonarola instituted strictly puritanical laws in Florence, including against sodomy... but that was applicable to hetero sex as well as homo. Of course, I wouldn't want to defend Savonarola's views in their entirety. He was not a modern democrat. But he and people akin to him - Munzer, Cromwell, the Levellers, the Diggers... the p/Protestant revolutionaries of the era of transition from feudalism to capitalism - were more than just foaming fanatics. They meant more than that. Of course, revolutionary ideals are always depicted as fanatical and dangerous in mainstream culture, more horrible by definition than any status quo they may challenge. c.f. anybody in Gotham City who doesn't like draconian laws and huge imbalances of wealth.
On the subject of Savonarola, we of course get a depiction of the revolution he led in Florence against the Medicis as an irrational explosion of fanaticism and lunacy. We get no hint of the scale of corruption and oppression committed by the Medicis, no real hint of the horror of poverty in Florence alongside the amazing cultural flowering and explosion of wealth. We get nothing about the popular support for Savonarola, the support of artists like Michaelangelo and Botticelli (we even get Machiavelli and Cesare tutting over the burning of a Botticelli on one of the Bonfires of the Vanities). The Florentine republic created after the people kicked out the Medici was astonishing for its time. The franchise was extended, public office was opened to lower ranks, the use of capital punishment was limited, etc. None of that. Natch.
So, moral ambiguity at all costs... even at the cost of any moral compass in the drama, or any semblance of historical truth. There are, I think, worse sins in drama than areas of moral clarity.