Somehow I didn't cotton to this when I was reading 12K five years ago, and certainly not when I was watching the anime err whenever that was, but the reason you have different kanji for king's/ kirin's name and country name isn't entirely 'country's precious forbidden name kanji, therefore use a homonym'. That may enter into it, I suppose, but I think it's more that the king/ kirin and the country are different entities. You call the king after the country, yes of course, but you wouldn't use the same kanji because that implies the king/ kirin and the country are *the same thing*. And of course they're not.
Somehow this is perfectly clear in my head while reading and oddly difficult to express otherwise.