Maybe just the timing? No actual person would be actually mad about something like this. If it was done right after any random person’s death with the knowledge of the person’s death it could be seen as in slightly bad tastes. Knowing it was produced beforehand though makes it more wholesome but just unfortunately timed. I personally think it’s something the pope would have liked given that Luce exists as an official church anime character. I don’t know why the actual person removed it, but it could be they thought the timing was not so great.