The Story of Bob does have an adequate answer in the "vocabulary of harms". The implicit claim that it does not echoes claims of Jonathan Haidt in much of his work on morality, especially his "five pillars" theory and subsequent extrapolations which have been eagerly seized upon by conservative proponents as evidence that liberals are narrow-minded.

It therefore irritates me a great deal when I see such claims going unchallenged, despite their (to me, anyway) obvious inaccuracy.

Here, then, is my "harm/care-based moral system" take on The Sacrifice of Bob:

I'm going to presume that the fictional culture in the story is reasonably happy and prosperous, otherwise we would have been talking about how terrible their culture is even before the sacrifice had taken place.

• (1) Given that this fictional culture and its president have a good track record at keeping the peace (in diametric opposition to certain other presidents whose similar but much less moral actions are implicitly being referred to), and that Bob's sacrifice probably saved millions of lives, there is nothing wrong with the President's action -- certainly nothing worse than that of a general sending a soldier into a known death trap.
• (2) Given that this culture seems to achieve goals we value (reasonably happy, prosperous people) while using morals we find questionable (highly authoritarian), I should think that we would want to study them intently to see how they do it. Perhaps we can learn some things -- or perhaps the appearance of happiness and prosperity will turn out to have hidden costs.

Having now played a turn by the rules, I have a bone to pick with the basic concept.

The problem with such examples is that you are basing an implicit conclusion -- "harm-based morality is limited" -- on a fiction, a lie. It's a complex form of circular reasoning: "Imagine a world in which this particular form of morality inexplicably produces positive results. Don't you feel silly trying to defend your morality now?" or even "Imagine a universe in which the earth is a flat disc riding on the back of 4 elephants. How can you stick to your narrow-minded idea that Earth is a spheroid orbiting the sun when in some other universe it might not be?"

All that said, I think I agree with the ground ground rules you propose at the end. I have always said that inability to explain one's reasoning doesn't prove one wrong, and that science needs to pay more attention to intuition (reasoning based on summed data for which complete records were not kept) -- but there do need to be guidelines, because intuition should no more trump science unilaterally than the other way round.