Of course this would depend on the person but I would argue that for most people the love of family would be stronger. Even in a situation like the sniper finds himself when he comes face to face with what his commitment to his country has cost him, I would guess that his heart was broken.
Here was a young man who had shown extraordinary dedication to the Republican cause in the Irish Civil War. He was willing to endure hunger and willing to risk his own life in order to accomplish his mission. He was willing to kill civilians because they were helping the other side.
And of course O'Flaherty ends the story before the reader can get a glimpse of the sniper's reaction to finding that he killed his brother. But my guess would be that he would immediately question the value of his cause in a way and with an urgency he didn't before. Even if he'd known that his brother was fighting for the other side, the reality of it could perhaps be avoided until this moment when it stared him directly in the face.