Could it be said that "The Boy in Striped Pyjamas" contains a form of irony in the way that Father thought he was killing the enemy; not his son?

Indeed, the ending to "The Boy in the Striped Pajamas" is
ironic.  It's painfully ironic.  If we operate on href="http://www.bartleby.com/116/102.html">H. W. Fowler's definition of
"irony" such as, "that the surface meaning and the underlying meaning of what is said
are not the same," we can apply Fowler's understanding to Boyne's novel.  The fact that
Bruno's father operates as an extension of the Nazis, promoting its values and living
his life in full confidence of what is being done in the Holocaust, would represent a
surface meaning of the narrative.  Running contrary to this surface meaning is Bruno's
befriending of Shmuel.  The fact that the father's orders to round up the prisoners for
mass execution would involve his own son, wearing "pajamas," is ironic because the
surface meaning of the father's actions contrasts with the underlying meaning and the
implications of them.  He is left to fully understand this at the end of the novel.  The
historical irony that is also present is that the Holocaust ended up killing both the
victims and the agressors' sense of humanity.  When the father recognizes this, he might
actually be mourning for both his son and his son's dignity.