Later, Mills was ensnared in the state's Old Court – New Court controversy wherein the state legislature attempted to abolish the Court of Appeals in retaliation for its opinion overturning a piece of debt relief legislation. The legislature established a new Court of Appeals, and for a time, both courts claimed authority as the court of last resort in Kentucky. The controversial measure abolishing the old court was repealed in 1826, and Mills resigned from the court in 1828. He died suddenly of an apoplectic stroke on December 6, 1831.
Mills married Mary Read Thornton. One son, Thornton Anthony Mills, was born in September 1810. Another son, Benjamin Mills, was born June 23, 1820. The family attended Paris Presbyterian Church, and both Benjamin and Thornton became Presbyterian ministers. Benjamin also served as a brigadier general in the Union Army during the Civil War.
His nephew Joseph Trotter Mills, Wisconsin State Assemblyman and jurist, lived and studied with his uncle.
Mills served for a time as president of Washington Academy (now Washington and Lee University). Later, he moved to Bourbon County, Kentucky with his father. He abandoned the practice of medicine and studied law, commencing practice in Paris, Kentucky around 1806. He served six one-year terms in the Kentucky House of Representatives—in 1806, 1809, and 1813 through 1816. In 1816, he failed to secure a seat in the United States Senate, losing to Isham Talbot by three votes.