Morrison had been an early supporter of the reform movement in Upper Canada and participated in meetings to encourage political change. He spoke repeatedly against armed rebellion and encouraged William Lyon Mackenzie to continue soliciting support for his reforms. He did not participate in the Upper Canada Rebellion and remained in his home instead. Nevertheless, he was arrested and charged with treason for planning and executing the rebellion and found not guilty at a subsequent trial. Fearing additional charges, Morrison fled to the United States and resumed practicing medicine. When amnesty was granted to most participants of the rebellion in 1843, he returned to Toronto to continue his medical practice and serve on various boards of medicine. He died on March 19, 1856, of palsy in Toronto.