Scott, what George stated I also agree with as I do not see a Thomas Halligan in the Confederate Army only the one in Georgia. However after doing some brief looking I did see a man who fits your description living in Clifton Forge,Va. which is in Allegheny County just across from the West Virginia border in the 1910 United States census. Thomas Halligan was living with his son J.E. Halligan and was listed as being born in 1835. What struck me as a little odd was that his son (J.E. Halligan) was shown as being born in Pennsylvania in 1857. It also stated that his father (Thomas Halligan) was also born in Pennsylvania. In looking at the 1860 census I did see a Thomas Halligan living in York, Pennsylvania and sure enough there was a Joseph E. Halligan listed as a young child and he was married to Mary, also Thomas Halligan had a wife named Mary who died in 1888. According to Find A Grave the Thomas Halligan buried in Allegheny County, Virginia also had a wife named Mary and she too is buried at the Crown Hill Cemetery in Allegheny County, Virginia.

Thomas Halligan's father was born in Virginia. Some Confederate Soldiers did fight for the Confederacy from Northern States. However, in this case I believe if he was in the War he may have fought for the Union. There are several Thomas Halligan's who fought for the Union. I did see where there was a Thomas Halligan born in Virginia in 1835 on one site however after looking at various sites research does seem to indicate that he may have been a Union Soldier. It appears that he died in Freeman, West Virginia in Mercer County on January 4, 1923 and was buried in Allegheny County, Virginia. It would not be the first time a Union Soldier had a Confederate marker.

Scott, I'm not 100% sure of this however I would be open minded that he may have been a Union Soldier if a soldier at all. The brief research I have done seems to lead in that direction. You will have an interesting story if this turns out to be the case. Good Luck!