Both sides sometimes had to play rough, but I feel that the Confederates shed much more blood of its own people than the Union did. Part of this was undoubtedly due to the fact the reb areas contained almost all the armed conflict, but I think that the nature of the CSA lent itself to the prominence of a class of stay at home parasites who enriched themselves while better men put their lives on the line in fair combat.
There is very good evidence that some of the Unionist and Abolitionist in Texas poisoned wells, and did some acts of sabotage.
If that is the case, then hanging them would have been justified.