Presidential diaries would be another example, or a CEO's Rolodex.
Both retention and publication go against the wishes of the deceased, but I would see putting them in the Vatican Archives for a few researchers to peruse as a lesser transgression than putting them in a book for all to see.
I agree with you that there is probably a legal or moral requirement to retain the notes of Pope John Paul II, and that may override his personal wishes (though, again, in an archive, rather than in all good bookshops).
You are also correct that it may be difficult, or even impossible to separate JP2's notes from Karol Wojtyla's notes after 1978, but what about before? Are the notes of Bishop of Ombi or the Archbishop of Krakow also as important? How far back does the corporate entanglement go?
In any case, the question of why it is that way doesn't much matter for this particular question. Regardless of why copyright applies to a dead guy's works, it does.
That may depend on whether they are John Paul II's notes (and the Bishop of Ombi's etc.) or Karol Wojtyla's. And whether the published work belongs to The Church or to Dziwisz.