Well the thing is, by the time Rin dies and Obito turns we know that Madara is in control of at least some portion of the Hidden Mist. We don't know how many he controls or if its just a single squad. We don't know if the history of the "Bloody Mist" goes back all the way back to when the village was formed or not. Though I'd say its safe to assume that it started at some point following the death of Gengetsu, the Second Mizukage. Reasoning for this is mainly that Gengetsu was a member of a clan known for using rather exotic techniques that while they've never been referred to as Kekkai Genkai, but rather "unique" to them it speaks somewhat volumes.
Another reason is Gengetsu's early death and personality by itself as we saw during the Fourth Great Ninja War. While a man of pride, he wasn't above praising other people and helping them grow as people and in fighting ability. He truly was what a Kage should strive to be in almost every regard and I find it hard to believe that such a person would inn act a system where people slaughtered their friends on command. His early death might also explained why and how the village changed so quickly as he didn't have much of an effect on the village that we know of, much like Minato.
Another thing about Gengetsu's personality that makes me seriously doubt he ruled during the time it was called the "Bloody Mist" is how he talks to Mu. He clearly doesn't get along with Mu on a personal level or a professional level and what we see of Mu is a man who is willing to stoop to just about any low to protect his village and people, refusing to work with other people over the risk that might betray him at some point. That is the exact thinking the Bloody Mist incorporates and Gengetsu seems extremely opposed to it.