@UnluckyGrape: Exactly. True villain MC's are near impossible to pull off.
The main reason is besides a REALLY niche audience that just like to watch good people suffer most don't like to root for genuinely terrible people. Video Games get away with this a little easier by either creating multiple endings so the bad one is just a "what if" or just making the player entirely responsible for the bad stuff so they don't hate the MC for doing it.
But there are a few other ways writers try to get away with genuinely evil MC.
1. make their opponents even worse so the MC becomes the lesser of two evils. Many "REVENGE" stories take this route with the MC's revenge targets being cartoonishly evil in order to justify the MC killing even innocent people as collateral if it means getting rid of the real monsters. Or at least justify the MC's insanity as being caused by the true evil.
2. Make the MC insane in such an entertaining fashion you kind of enjoy seeing what madness they do next even if it means other characters die. Case in point in the JOKER from Batman. He is obviously evil in 99% of his incarnations but people still tend to like him anyway. They don't root him for, but people still buy comics with the Joker as the MC to get a deep look at his inner madness.
3. They make the MC a lawful evil. Because they still have A moral code audiences can grab onto that and root for the MC even if they are willing to do evil things to accomplish their end goal.
I could go on but I think people get the point.
In Nana's case I think the writers started out trying to make her appealing with the "Lawful Evil" angle as she's evil but is supossedly following a moral code. The PROBLEM though is the very foundation of that moral code is rather flawed and is seemingly contradicted with her first two victims. This was the author's first mitake. Nana's victims should have been murderious psychopaths that deserved to die in order to legitimize her actions in the eyes of the audience. With the good and innocents dying afterwards to establish her willingless to kill anyone and everyone regardless of innocent or threat level.
Because the author did it in the opposite way Nana failed to make a good impression with the audience. Hence why the story couldn't survive without her switching sides as there was no way to get the average reader to side with her actions.
The author's other mistake was establishing from the start that she's doing all this at the council's order. While in theory this would help reduce her guilt and put it on the council it also strips away any hope she had of being LAWFUL EVIL because she has NO morals or rules she acts by ... she's just following someone else's orders and thus there is no apparent personal ethics for the audience to see.