I just watched a program on the history channel about terrorist acts during the civil war, including bio-terrorism. They describe a doctor named Luke Blackburn who tried to spread Yellow fever in the north and among union troops by distributing infected clothes, of course at that time they didn't know yellow fever was not contagious but was spread through mosquito's. He was captured, but at the end of the war was released and was hailed as a hero and eventually went on to become governor of Kentucky.
They talked about plots to kill Lincoln and Jefferson. One which was carried out one day before Lee surrendered. The two men were captured on their way to blow up the white house.
Another interesting case was the one about the Sultana, a Mississippi steamboat that was blown up on April 26, 1865. There were over 2400 people on board, 1800 died. It was considered the worst act of terrorism on American soil until 9-11. The sad thing is, is that most of the passengers were soldiers who had been liberated from Andersonville and were on their way home.
They also talked at length as to wether Shermans March to the sea was an act of terrorism or war. the general beleif of those interviewed was that it was not, as most of the murder/rape/pillaging was done on an individual basis and not advocated by Sherman or his lieutenants.