The Taliban used a non-descript uniform that was only identified by a blue head dress. Hard to tell military personel from civilian.
Regardless of what the military wore or looked like, criminals are tried under a completely different set of laws according to Islam.
Hanging, stoning, beheading are all appropriate sentences as the religious ramification, no entrance into Paradise, is the goal.
After the executions, the corpse should be wrapped in pigskin and buried.