For the first two murders that the Butcher committed with Millie's body, Millie is actually home free. Millie opened the cryo-chamber that Ryler died in, getting the Butcher's physical fingerprints on the crutch and controls. With Mr Bernardi, the Butcher didn't touch anything in the shop that Millie wouldn't have anyway during class - if distinct fingerprints could be discerned at all. The only exception would be Mr Bernardi's body, but the Butcher only touches him on his clothing (when shoving him through the table saw, she grabs him by the ankles, over his socks, not his leather shoes), and CSI aside, it's actually very difficult to get fingerprints off woven cloth. However, for the murder weapons used at the Mill, Millie will just have to put her trust in law enforcement knowing that the Butcher was around (there's at least two officers besides Charlene to testify to that), and that the town wouldn't have a dedicated forensic expert anyway.
The fact that the Butcher is killing people in Millie's body means that Millie could have been arrested if anyone had seen the murders take place and reported them to the authorities. Thankfully, Millie continuously showing up near the crime scenes in the Butcher's body means that the Butcher is automatically held responsible, and the only people who thought otherwise were the Blissfield Butcher's actual victims.
