It isn't as clever as it thinks.

If an omnipotent God could arrange such an explosion, and we presume Him loving of all sentient creatures, He could easily arrange His explosion to avoid harming His creatures. Such a story wouldn't happen in the first place.

But what if He did? Anyone reading the Bible -- as certainly a Jesuit would have -- knows there is no theological requirement in Christianity that God value a life as humans value a life. "My ways are not your ways, says the Lord." St Paul is explicit that the notion that Pharaoh was created entirely for the demonstration of God's power by Moses does not contradict the justice of God. (Nor does he say Pharaoh was created for that purpose; he doesn't know, and treats the possibility as a hypothetical.)

Nor need the civilization's members be created simply for some demonstration. Perhaps they suffered the judgement of Sodom and Gomorrah. Perhaps the nova was the End Of The World for _that_ civilization, a component of its Second Coming, just as (Christians believe) our world will eventually experience. Genesis, Exodus, Paul, Revelations each provide precedents for such an apparent catastrophe. The priest can easily imagine any number of explanations consistent with his faith. (Indeed one might be the light of one world's closure illuminating the opening of another, reminiscent of the Greek's beacon signaling the fall of Troy in Aeschylus' "Agamemnon".)

Whether we look at the story from God's end or the priest's, it doesn't make any sense.

The reader doesn't need to _like_ any of those possibilities. The point is that the values by which we like or don't like anything are not necessarily the same as those of God. C.S. Lewis imagines a devil overseeing temptation during WW II saying "I am not in the least interested in knowing how many people in England have been killed by bombs. In what state of mind they died, I can learn from the office at this end. That they were going to die sometime, I knew already. Please keep your mind on your work." ("The Screwtape Letters".) For Lewis, death doesn't mean the same thing to God as it does to us.

Still more, the Christian thinks the perspective by which we judge doesn't know all that He does. Many very clever people have pointed out that a super-intelligence will think differently than we do. Boethius argued (in the sixth century) that God's different experience of Time can explain the apparent contradictions of omniscience and free will. That lightweight Godel argued out that what is logically contradictory for us, trapped in sequential thought, can be resolvable by an infinite knowledge that is beyond sequence. More recently (and casually) Vernor Vinge posits (in "A Fire Upon The Deep") that the study of super artificial intelligences will be classified as "theology".

And the reader doesn't even have to buy any of that. That's what tolerance is about, we're all free to form our opinions and arguments as we think best.

But it is just ignorant to, well, ignore those opinions and arguments that we don't agree with.

And it is remarkable how many supposedly intelligent, curious and tolerant people become so ignorant of what careful and intelligent people have thought when the topic is theology.