As we've said in "Reading the story allegorically," the penal colony itself is often read as an allegory. If you do that, you'll read the whole story as an allegory. And you can do that in multiple ways. We've already described how Austin Warren read the penal colony as "the world full of sinners."
Another way to read it is a quite different interpretation of the colony as a "totalitarian society" – think the USSR, Nazi Germany, or the world of 1984. As in a totalitarian society, the people inside the penal colony are kept under tight control by brutal methods of torture. As in a totalitarian society, too, there's no real justice, though there's supposed to be – you can be sentenced without trial or defense. There's also that way in which totalitarian societies tend to make their leaders into godlike figures, worthy of reverence: just like the old Commandant. In that reading, the officer himself becomes a victim of brainwashing, and the explorer is right to be horrified.
This reading is a bit less of a definite, or "strict," allegory than Warren's, because it doesn't make everything in the story "represent" something quite different (equating the old Commandant with God, for example). The penal colony could literally be called a totalitarian society, just on a very small scale.
Still another way to read it is kind of a cross between the two. The penal colony isn't a totalitarian society with a false religion, so much as a traditional religious society, held together by a brutal-seeming set of religious practices like ritual sacrifice. We, for ourselves, think this might be the best way to go, though we wouldn't identify the penal colony with any particular society. This way of seeing the story leaves readers (and the explorer) open to deciding for themselves whether there might be certain true or compelling elements in the society's practices, regardless of how ugly they look on the surface.
Or is it just barbarism after all? Maybe, at the end of the day, the penal colony is just what it seems: a gruesome, horrible, inhumane place.