I am reminded of a line from the comics of the cartoon Gargoyles, from the mid 1990s. In it, a reawakened King Arthur notes that many myths are based in fact, but few myths are accurate.
If we take the Dresden-Bible as a long accounting of myths, a long story translated and mistranslated over centuries, not everything should be taken as absolutely correct. What Pharaoh was doing and what was done to him is all speculation. Add in, if the Greek Gods exist, dollars to donuts so did the Egyptian Gods of that time. We just don't know their plot in what Pharaoh did.
As for which path was the least evil, I still favor Mab in that she is a controlled person. She doesn't like waste and stupidity. The killing of many uninvolved brings unwanted attention. Several of her former Knights were serial killers. Some of those kills could have been by the Knight's own choosing, and their stupidity brought in the mortal police who dispatched him.
Nicodemus encourages stupidity, he encourages people to believe he is a savior while he maims them and has his daughter rip out their tongues. He keeps them locked up, ignorant, frightened and alone. And he's been doing it for thousands of years.