NCIS used this trope to an extent with Gibbs, but it wasn't entirely aggravating because Gibbs's "gut" is established early-on as a "given"--and also because Gibbs is capable of doubt. (In the same way, Saitama's incredible power--a "given"--is a source of angst.)
The trope gets more aggravating when the reader is supposed to accept that a couple is broad-minded and tolerant yet...isn't it amazing how many characters who simply disagree with the couple end up suffering terrible ends? Rather like Victorian "bad" children who choke to death or fall down wells.
A series that I otherwise liked up to the last book became so vindictive in this way, I become increasingly uncomfortable. When the 2 male characters decided to get married and selected a pizza place for the reception, I thought, "Well, that pizza place better not make the mildest objection--not even being closed that day. Otherwise, it's going to burn down!"
I've encountered this "God or fate delivered just punishment to the people we despise" idea in religious fiction (which supports growing proof that the fundamentalist right and progressive left are staffed by the same types of people).
In either case, what is happening is not tolerance or compassion. For that matter, it's not good versus evil. It's not as magnanimous as the former or as big-picture, difficult, and objective as the latter.
It is rather a run amuck version of high-schoolers-clawing-up-the-social-ladder.