From reader Nate Winchester. Basically, if nuking a city is so bad, what about God essentially 'nuking' the human race except for one family back in the days of Noah? If nuking innocent civilians is intrinsically evil, wouldn't flooding away civilians - some of which, children at least, had to be innocent - also be intrinsically evil? I admit, I'm probably not qualified to answer this, at least from a Catholic point of view.
I would say the first point that would need hammered out is exactly where the Church stands on biblical criticism. After ten years, I don't know the answer to that. Most Bible study guides, biblical commentaries, and books I've read appear to be at least somewhat friendly to the critical approach to biblical scholarship.
By critical I don't mean criticize it like sometimes happens on the Catholic blogosphere, with insults and false accusations. I mean critical in the academic sense, analyzing the texts of Scripture to unpack its original meaning, what stories were or were not intended to be taken literally, which events did or didn't happen, which parts of what books of the Bible were written by the traditionally attributed authors, and which were patchworks put together over time. That sort of critical scholarship.
Almost every Catholic book I've read or been given seems to accept at least some of the more modern approaches to critical scholarship. Some have been pretty extreme, and almost would seem to run parallel to a commentary by Bultmann. Heck one even suggested that the New Testament books may have been written decades into the 2nd Century, and the Church merely lied about the Apostolic authorship to give heft to the argument for their inclusion in the Canon. Yeah. Lying to save children is bad, but the Church lying to get the books it wanted into Sacred Scripture is just hunky-dory. That book, by the way, was given to me by a local priest and had an imprimatur, just saying.
Anyway, it depends on how you approach the biblical texts. How much modern biblical scholarship do you accept? If you regard the Flood narrative as myth or fable, based on some vague Near Eastern natural disaster that made its way through the stories over the ages, and that some wag finally mixed with a Hebraic spin or two, then you'll have no problem. The Flood never happened as described, God is off the hook, back to the debate.
If you take the story as presented biblically, and understood historically, at least pre-critically, then that would be an interesting question. I wonder if anyone out there does accept the historically literal approach to the Flood narrative while also rejecting the decision to use the Atomic bombs on Japan. I'd certainly be interested to hear the take. My brief time spent Googling any articles along that line yielded a big goose egg.