His service as Chief Justice ended in 1851, and he practiced law in Santa Fe, as he would during much of his life, and also served as a district attorney during the American Civil War.
He made numerous political enemies, and his rulings regarding property confiscated during the Civil War were widely criticized as contrary to basic legal principles.
[13] In 1847, Houghton presided over several trials for treason resulting from the Taos Revolt, an insurrection against the American occupation that culminated in the assassination of Governor Charles Bent.
[14] Houghton's dramatic sentencing of conspirator Antonio Maria Trujillo to death by hanging has been frequently noted by historians:[15] Antonio Maria Trujillo:—A jury of twelve citizens, after a patient and careful investigation, pending which all the safeguards of the law, managed by able and indefatigable counsel, have been afforded you, have found you guilty of the high crime of treason.
Yet, while each and all were not only willing but anxious that you should have every advantage placed at your disposal that their highly responsible duty under the laws to their country would permit, you have been found guilty of the crime alleged to your charge.
For such foul crimes an enlightened and liberal jury have been compelled, from the evidence brought before them, and by a sense of their stern but unmistakable duty, to find you guilty of treason against the government under which you are a citizen.
Commanding the majority, Houghton wrote much of the constitution himself, which contained a declaration against slavery and a total rejection of land claims by Texas to portions of New Mexico.
[20] Their political dispute was largely rendered moot when the bid for statehood was ended by the Compromise of 1850, which instead organized New Mexico Territory, and provided that the issue of slavery would be decided by popular vote.
Houghton's service as Chief Justice ended March 1, 1851; the incoming governor of the newly formed Territory, James S. Calhoun, believed the provisional court to have been abolished by Congress.
Houghton tried to have him removed as governor, in part by alleging that Calhoun took sides with wealthy natives and Catholic Church officials against American residents.
[24] After leaving the bench, Houghton practiced law in Santa Fe, and helped form the Historical Society of New Mexico.
[28] He was named the wartime district attorney for New Mexico on September 19, 1861; he zealously got indictments for treason against several prominent citizens who he believed were southern sympathizers, but was unable to obtain any convictions.
[31] Houghton was also widely denounced for his handling of numerous lawsuits involving property confiscated during the American Civil War.
[35] Upon taking office, President Grant replaced the entire court, appointing Abram Bergen to Houghton's seat.