I think they made it that way largely because they wanted all of the various settlements to have their own unique character that would be universal across the game for everyone. Basically all of the settlements have at least some kind of structure that isn't scrappable without mods. They didn't want the settlement system to take away from the world that they actually envisioned for the game. I've seen tons of different builds at Sanctuary in different groups and articles, and they're all immediately recognizable as Sanctuary because of the houses. I've seen other builds by people who have used Spring Cleaning to scrap everything in the whole settlement too. Some of them have been awesome builds, but they're not Sanctuary anymore.
It's still a mod, but I'm using the Repairable Sanctuary mod. It fixes the houses. It doesn't restore them to their prewar condition, but it fixes the roof so that it actually functions as a roof, and fixes the holes in the walls so that they're all solid. It still looks worn and somewhat patched though. When I got back to Sanctuary from Concord and saw them start hammering on the houses, I naively thought that the houses were actually going to be repaired over time. This makes it look more like they've actually accomplished something with all that hammering. It maintains the character of the original Sanctuary, but makes it a bit easier to work with.