The sniper, the only way he's referred to (other than as "the Republican sniper"), is the main character and in that sense, he is the protagonist. The "enemy sniper," as he's referred to is essentially the antagonist. The sniper is essentially alone in this story and this solidifies his characterization as the main character and protagonist. He has to deal with the "enemy sniper," an old woman (the informer), and the enemy soldier in the turret. While "the sniper" is the main character/protagonist and the "enemy sniper" is the antagonist, the concepts of "good guy" and bad guy" are not as clear. This is the Irish Civil War (Republicans versus Free Staters) and is therefore a war of brother against brother. After the sniper kills his enemy, he wonders if he might know his victim. The story ends with this realization:
Then the sniper turned over the dead body and looked into his brother’s face.
This can be taken literally or figuratively. Either the sniper killed his actual brother (the common assertion) or he realizes the significance of killing one of his own countrymen, perhaps close to his age. And although in historical retrospect we might say that one side in a civil war was right and the other was wrong, the idea here is that we have two young men killing each other, two men that could very well be brothers. Because they are young men (the sniper has the "face of a student"), they may have been forced to fight and/or they find themselves battling in a war that was instigated by forces larger than themselves. In this case, they both might be considered the "good guys" in that they probably did not choose to find themselves in a situation of brother against brother.