My SMITHs (Scotland, Caledon twp, East Garafraxa twp, Amaranth twp) were also from Amaranth but they are a different family then you are working on. I was able to do some work on your family yesterday and I am happy to say I was able to answer some of your questions.
I found two Thomas SMITH deaths in the Orangeville Sun index in the range 1861-1871 but neither of these were yours. I did find one more Thomas SMITH from another source who I believe is the one you are looking for:
Thomas SMITH, 82, Amaranth, Interment date: Mar. 14, 1868, Burials - St Mark's 1850-1872, Page: 4 , Book: D
I have no other burial information for this Thomas. I do believe his wife is Mary. I found two marriage records:
County Marriage Registers of Ontario, Canada 1858-1869 Volume 12 Simcoe County:
Groom: Wm. SMITH, 30, Amaranth, Co. Tyrone, Ireland, Thomas & Mary SMITH
Bride: Annie CAMPBELL, , Orangeville, Tyrone, Ireland, James & Jane CAMPBELL
Witness: James CAMPBELL, Orangeville & Jane CAMPBELL
August 16, 1860
County Marriage Registers of Ontario, Canada 1858-1869 Volume 10 Wellington County:
Groom: James SMITH, 35, Amaranth, Ireland, Thomas & Mary SMITH
Bride: Matilda HALL, , Amaranth, Mono, William & Mary HALL
Witness: Samuel A. CARSON, Orangeville & Sarah COLAGIN, Amaranth
October 19, 1864
I cannot account for the William SMITH in the 1881 census, he might be an uncle or a cousin, because the William SMITH who married Ann CAMPBELL died in 1880.
Greenwood Cemetery, Orangeville
SMITH - Annie SMITH 1869-1940. Mary SMITH wife of George SAXTON 1866-1931
William SMITH 1823-1880. His wife Annie CAMPBELL 1832-1907. Natives of County Tyrone, Ireland.
Thomas SMITH 1862-1887. Jean SMITH 1868-1931.
Now the surprise newspaper article that explains what happened to brothers John and James SMITH.
Shelburne Free Press, May 24, 1888, DEAD: James Smith, of Lot 12, Con 1, Amaranth, died on Sunday, May 13th, after a long illness. He was a brother of John Smith, the victim of what is known as the Shelburne "murder case," which occurred in January, 1882. A son of the deceased was tried for the murder, but was acquitted. It is the general opinion that James Smith knew all about the murder, and was credited with planning it. If such was the case, he died without telling his secret.
Using Ancestry there is a death record for John SMITH who died: January 21, 1882 in Dufferin - cause of death - Murder (shot in the head).